BEGIN --> chmbbs-jan93.log <---
I am a first year grad student at PennState University, and at present
I am trying to perform some CHARMm calculations (with Polygen QUANTA) on
metal-carbon clusters. My problem is how can I obtain the correct paramaters
for metals such as Ti, V, and Zr to do these calculations. Thank You.
brian@opus.chem.psu.edu
I would like a reference that lists the parameters used in the
CHARMM potential energy functions:
a) charges q, polarisability alphas, and vander waals radii for
each atom type and a description of the atom types
and
b) the force constants and eq. property values for the torsional,
bond stretching terms etc.
thanks in advance,
shahul h. nilar
biotechnology resarch institute,
national res. council of canada,
6100 ave royalmount ave
montreal h4p 2r2
canada
From nauss@wrair-emh1.army.mil Fri Jan 8 14:12:54 1993
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Date: 8 Jan 93 13:35:00 EST
From: nauss@wrair-emh1.army.mil
Subject: Public domain or academic versions of CHARMM
To: "charmm-bbs" <charmm-bbs>
Status: R
Currently, I am seeking an academic position at a small college or university
where I can continue my research in computer modeling of biological molecules.
A question that comes up regularly is the cost of the high-powered software.
Can anyone provide a point-of-contact (name, address, telephone number, and
e-mail address) for obtaining a public domain or academic version of CHARMM?
Either the NIH or Harvard dialects will be satisfactory. Will there be any
fees such as licensing fees? What platforms can they run on?
Jeff Nauss
--------------------------------------------------------------------------------
E-mail address: nauss@wrair-emh1.army.mil
Mailing Address:
Department of Gastroenterology
Division of Medicine
Walter Reed Army Institute of Research
ATTN: MAJ Jeffrey L. Nauss, Ph.D.
Washington, D.C. 20307-5100
Telephone: 202-576-3485
Recently, I have attempted some molecular dynamics simulations of different
linear peptides and cyclic compounds. I am using Quanta version 3.2 and CHARMM
21. I have attempted to run these simulations at elevated temperatures to cover
a wider area of conformational space. Unfortunately, I have often seen wide
temperature fluctuations during the equilibration phase as velocites are
scaled. Sometimes these fluctuations will be between O and 9000K! For example,
suddenly, CHARMM will report that the velocities are being scaled from say 600K
to 0K and neither temperature is my equilibration temperature. The next
equilibration step or cycle the CHARMM reports that the scaling is from OK to
600K. And continues to cycle in this manner.
Other times, the system may equilibrate satisfactorily (or at least it appears
so to me) then during the actual simulation, the temperature will slowly
increase to over 10,000K and the molecule is, of course, destroyed.
I have examined my script files and attempted several variations to correct
these problems. But to no avail. Does anyone have any suugestions on what may
be wrong? Any ideas on tests that I could perform? I will not bias anyone by
stating what variations I have tried. I am looking for fresh ideas and am
becoming desperate.
Thanks for your time and thoughts...
Jeff Nauss
--------------------------------------------------------------------------------
E-mail address: nauss@wrair-emh1.army.mil
Mailing Address:
Department of Gastroenterology
Division of Medicine
Walter Reed Army Institute of Research
ATTN: MAJ Jeffrey L. Nauss, Ph.D.
Washington, D.C. 20307-5100
Telephone: 202-576-3485
Currently, I am seeking an academic position at a small college or university
where I can continue my research in computer modeling of biological molecules.
A question that comes up regularly is the cost of the high-powered software.
Can anyone provide a point-of-contact (name, address, telephone number, and
e-mail address) for obtaining a public domain or academic version of CHARMM?
Either the NIH or Harvard dialects will be satisfactory. Will there be any
fees such as licensing fees? What platforms can they run on?
Jeff Nauss
--------------------------------------------------------------------------------
E-mail address: nauss@wrair-emh1.army.mil
Mailing Address:
Department of Gastroenterology
Division of Medicine
Walter Reed Army Institute of Research
ATTN: MAJ Jeffrey L. Nauss, Ph.D.
Washington, D.C. 20307-5100
Telephone: 202-576-3485
From ryszard@MSI.COM Fri Jan 8 18:29:45 1993
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From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9301082327.AA10759@hogan.MSI.COM>
To: charmm-bbs
Subject: QUANTA/CHARMm and metals
Status: R
Brian,
One way is to take parameters from parameter files and
if some are missing do your own parametrization...
Ryszard
From bobf@MSI.COM Fri Jan 8 18:46:32 1993
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From: bobf@MSI.COM
Message-Id: <9301082343.AA14669@support>
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: charmm-bbs
Subject: Re: parameters
Status: R
Shahul Nilar writes:
> I would like a reference that lists the parameters used in the
> CHARMM potential energy functions:
>
> a) charges q, polarisability alphas, and vander waals radii for
> each atom type and a description of the atom types
>
> and
>
> b) the force constants and eq. property values for the torsional,
> bond stretching terms etc.
>
If I understand the question properly, these values are all listed in the
PARM.PRM file in the data subdirectory. A listing of the atom types,
with a brief description of the intended use, is found in MASSES.RTF in the
same directory.
Bob Funchess
Opinions or statements contained in this letter are not to be construed as
official statements of Molecular Simulations Inc. Customers with current
maintenance contracts in place are welcome to contact the Molecular
Simulations technical support hotline at 1-800-756-4674.
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From sfleisch@hydra.convex.com Sat Jan 9 17:42:33 1993
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From: sfleisch@hydra.convex.com (Steve Fleischman)
Message-Id: <9301092240.AA15248@hydra.convex.com>
To: charmm-bbs%emperor@harvard
Subject: C21 versus C22 speed
Status: R
CHARMM Problem Report Form
Please use this form to report problems you have found in using CHARMM.
Send your problem report to charmm-bugs@tammy.harvard.edu
=========================================================================
Name : Stephen Fleischman
Email Address : sfleisch@convex.com
Institution : Convex Computer Corporation
Date : Jan. 9, 1992
CHARMM version : 23a1 (actuall 22)
Machine : Convex C series
Operating System : ConvexOS
FORTRAN version : fc 7.0
Optimization : default
Command(s) involved (including options used): dynamics
One-line summary : C22 was reported to significantly slower than C21r3
Convex version.
Detailed description:
There have been a number of reports that the Convex version of CHARMM 22 is
significantly slower than CHARMM21r3 available from MSI but actually
done at from Convex. There was also a report that this is true for the SGI.
I will not address that problem in this report.
One such report was from Prof. Ernst Mehler at Mt. Sinai Hospital.
So, using a benchmark derived from one of his test cases I constructed a
dynamics test. The test involves 100 steps of dynamics of calmodulin with
water resulting in 6817 atoms. This is not the exact system Prof. Mehler
tested but does confirm his observations. The original verlet integrator was
used and SHAKE was not. The fast nonbond routines were also used.
I profiled the jobs with both versions of CHARMM and found that in CHARMM 22
the program was using ENBFV8 not ENBF3 as in CHARMM21r3. This is due to the
fact that the input used the command FAST 1. This results in LMACH being
set to 1 and the vector routines by Youngdo Won (and predecessors) being used.
If FAST PARVECT or FAST 4 is set then LMACH is 2 and the parvect routines
by yours truly are engaged. Here are the resulting CPU times:
CHARMM 21 rev. 3: 21.27 min.
CHARMM 22 VECTOR: 28.78 min.
CHARMM 22 PARVECT: 20.57 min.
So the current solution is to specify FAST PARVECT or FAST 4 (35% faster in
this case.)
Ironically, FAST CONVEX results in use of the slower vector routines.
Go figure.
Also, the default for Convex versions coming out of Harvard is to have the
fast non-bond routines not be used.
In that case one needs to issue the command: SPECIFY FNBL ON.
This is not true for the MSI commercial version which is built at Convex.
There may be other causes for slow down with the use of the
newer dynamics routine and SHAKE. IF fast SHAKE is used it shouldn't be
too much of a problem.
I will at some point look at the fast scalar routines (since I need to
support HP now).
As Bernie Brooks and Milan Hodosheck have reported, the parvect routines are
also 10% faster on the Cray than the Cray routines.
Sample input to reproduce the problem:
Available upon request.
Other Comments:
Remove the vector and Cray ( :-) just kidding Charlie) routines.
From nauss@wrair-emh1.army.mil Fri Jan 8 14:12:54 1993
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Message-Id: <9301081912.AA12505@emperor.harvard.edu>
Date: 8 Jan 93 13:35:00 EST
From: nauss@wrair-emh1.army.mil
Subject: Public domain or academic versions of CHARMM
To: "charmm-bbs" <charmm-bbs>
Status: RO
Currently, I am seeking an academic position at a small college or university
where I can continue my research in computer modeling of biological molecules.
A question that comes up regularly is the cost of the high-powered software.
Can anyone provide a point-of-contact (name, address, telephone number, and
e-mail address) for obtaining a public domain or academic version of CHARMM?
Either the NIH or Harvard dialects will be satisfactory. Will there be any
fees such as licensing fees? What platforms can they run on?
Jeff Nauss
--------------------------------------------------------------------------------
E-mail address: nauss@wrair-emh1.army.mil
Mailing Address:
Department of Gastroenterology
Division of Medicine
Walter Reed Army Institute of Research
ATTN: MAJ Jeffrey L. Nauss, Ph.D.
Washington, D.C. 20307-5100
Telephone: 202-576-3485
From muegge@groucho.chemie.fu-berlin.de Tue Jan 12 08:39:59 1993
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From: muegge@groucho.chemie.fu-berlin.de (Ingo Muegge)
Subject: Re: Temperature Fluctuations & Dynamics Simulation
To: charmm-bbs%emperor@harvard
Date: Tue, 12 Jan 93 14:37:25 MET
X-Mailer: ELM [version 2.3 PL11]
Status: RO
Dear Jeff,
Do you have reset the nonbonded list often enough during your simulations?
The mobility of atoms increases with higher temperatures considerably.
It could be possible that your time step is to big at this temperature.
Which sort of equilibration you are using for the simulations?
An rather gentle way to heat up your system is by using Langevin dynamics.
You couple all or a portion of atoms to an external heat bath. That is calling
"quasi canonic". The scaling or assigning mechanism responsible for vibrations
of the energy and temperatur is avoided.
Ingo Muegge.
--
|~| Ingo Muegge | Freie Universitaet Berlin
/ \ muegge@harpo.chemie.fu-berlin.de | Institut fuer Kristallographie
/FUB\ phone +49 30 838-3890 | Takustrasse 6
`---' fax -6702 | D-1000 Berlin 33 Germany
From chandra@yorvic.york.ac.uk Wed Jan 13 08:17:22 1993
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Via: uk.ac.york.yorvic; Wed, 13 Jan 1993 13:14:51 +0000
From: Chandra Verma <chandra@yorvic.york.ac.uk>
Date: Wed, 13 Jan 93 12:22:12 GMT
Message-Id: <26731.9301131222@yorvic.york.ac.uk>
To: charmm-bbs
Subject: Hi
Status: RO
Has anyone implemented CHARMM (some recent version) on the intel i860 systems under NX/2 protocols.
- or in general under any multi-processor multi-memory systems. If so i would be grateful for any
help
thanx
chandra
From brbrooks@helix.nih.gov Wed Jan 13 11:01:30 1993
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Date: Wed, 13 Jan 93 10:59:04 -0500
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9301131559.AA09158@helix.nih.gov>
To: chandra@yorvic.york.ac.uk, charmm-bbs%emperor@harvard
Subject: Re: Hi
Status: RO
Chandra,
We have a version of CHARMM23 running on an Intel iPSC/860.
For 128 nodes, the efficiency is roughly 60% (factor of 80) using
a 12A nonbond energy cutoff.
Bernie Brooks
From tennantm1%frgen.dnet@smithkline.com Thu Jan 14 06:16:23 1993
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From: tennantm1%frgen.dnet@smithkline.com (Mike Tennant. Harlow x3328)
To: "charmm-bbs@emperor@harvard.harvard.edu"%INET.dnet@smithkline.com
Cc: TENNANTM1@smithkline.com
Subject: Langevin Dynamics
Status: R
Hi!
A quick, hopefully trivial, question! When using Langevin dynamics
with NO explicit solvent, i.e. just using the frictional effects to dampen
to atomic motions, does anybody know whether it is more 'correct' to
use a constant, as oppose to a distance-dependant, dielectric??
Mike Tennant.
Smithkline Beecham.
Coldharbour Road,
Harlow,
Essex. UK.
Email: tennantm1@phvax.smithkline.com
Greetings,
I'm uncertain to whom this message should be sent, so it's going to the
'emperor'. I have been having a tough luck in using CHARMM with small
organic molecules (not peptides). It seems that > 90% of the structures
wind up with missing force field parameters.
The reason for this message is two-fold.
(1) Can we distribute new parameters by this E-mail club?
(2) A recent paper (Karfunkel & Gdantz, J. Comput. Chem., 1992, 13,
1171-1183) relied heavily on QUANTA/CHARMM for small molecule and crystal
structure optimizations. I note that Karfunkel (Switzerland) is not on your
E-mail address list. He should be unless he does not wish to be. In the
paper is the statement "A copy of the force field parameter file in
CHARMM format (about 60 pp.) is available from the authors upon request."
I have written to Karfunkel requesting the data but at this moment have not
received a reply. Could the MSI and/or CHARMM front offices make such a
request?
Thanks,
Herman Ammon, phone = 301-405-1824.
We want to write distances between atoms to a file using WRITE TITLES.
We expected ?RAXI to be useful for this purpose (after filling the RAXI
variable with COOR AXIS), but find that when ?RAXI is put in a WRITE
TITLE title line, it is not replaced with a number. Instead, the
characters "?RAXI" appear in the file. Likewise, when the command
"SET 1 ?RAXI" is issued, the error message "RAXI is not an energy variable"
is issued. Is there a simple way to do this?
-Dave Busath and Steve Bogusz
One way is to use "quick" command which writes to output
followed by grep. Quick is described in miscom.doc.
Ryszard Czerminski, MSI
Dave/Steve,
If you can't get ?RAXI to give you what you want, try
COOR DISTANCE SELE ... SELE ... UNIT n
Where UNIT n is a card file previously opened.
Tim Mitchell
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax. (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || mitchell_t%frgen.dnet@smithkline.com U.K. |
-------------------------------------------------------------------------------
Origional query follows.......
From: INET::"BUSATH@BROWNVM.brown.edu" 19-JAN-1993 19:48:55.35
To: CHARMM-BBS%emperor@harvard.harvard.edu
CC:
Subj: distances
We want to write distances between atoms to a file using WRITE TITLES.
We expected ?RAXI to be useful for this purpose (after filling the RAXI
variable with COOR AXIS), but find that when ?RAXI is put in a WRITE
TITLE title line, it is not replaced with a number. Instead, the
characters "?RAXI" appear in the file. Likewise, when the command
"SET 1 ?RAXI" is issued, the error message "RAXI is not an energy variable"
is issued. Is there a simple way to do this?
-Dave Busath and Steve Bogusz
For all interested in detailed analyses of molecular dynamics trajectories and
some aspects of protein structures, there is a graphical program called SQUID
which complements the CHARMM analysis facility and makes life and MD much
easier to deal with. The reference is
J. Molecular Graphics, Vol. 10, (No.4), 247-252 ,1992: Author : T.J.Oldfield
He can be contacted at oldfield@uk.ac.york.yorvic for more information
* Script file produced by QUANTA
*
! Startup script for CHARMm
!
banner
bomblevel 0
wrnlev 5
prnlev 5
reset
open read unit 21 card name $CHM_DATA/MASSES.RTF
read rtf unit 21 card
close unit 21
open read unit 20 card name "jan.prm"
read param unit 20 card
close unit 20
open read unit 20 card name "jan.psf"
read psf unit 20 card
close unit 20
open read unit 20 card name "jan.ic"
ic read unit 20 card
close unit 20
OPEN READ UNIT 70 CARD NAME "jan.crd"
READ COOR UNIT 70 card comp
open read unit 41 file name "simul.DCD"
trajectory iread 41
set 1 1
label loop
traj read
coor rms mass
incr 1 by 1
if 1 lt 100 goto loop
open write unit 30 card name rmslist
set 1 1
label start
write title unit 30
* ?RMS
*
incr 1 1
if 1 lt 100 goto start
stop
########################################################################
I have just started using CHARMM22 standalone. I have managed to
calculate RMS-values from this CHARMM stream file, but how can I get
a file with a list/table of these RMS-VALUES with picoseconds/frames?
As you can see, I had a bad try with "write title".
I'll be grateful for answers.
Thanks in advance.
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
In the past, I have been more successful writing a variable if I set
it first. As in:
set 1 ?ENER
...
write title ...
* The energy is @1.
*
The listings I have do not show a ?RMS command, but if this works
in a print statement (but not the above "set" mechanism) then try
a redirect of the standard output unit the way QUANTA does.
Before the "write title" command issue the command:
outu 30
After appropriate print statements:
close unit 30
Any commands between the two statments get printed to unit 30,
instead of the standard output. Hope this helps.
Thanks to all who responded to our question on how to output a distance
between two atoms to a text file using WRITE TITLES. The problem was
that a title such as:
* @1 @2 ?RAXI @4
would not send the value of RAXI to the title. It complains that
RAXI is not an energy variable. One also could not use:
SET 6 ?RAXI
for the same reasons. I consider this a bug in charmm.
Using suggestions by others I tried a number of methods, many which
work but do not output the distance in a title with the other values in
one line (to make life easier by allowing me to import the values into a
spreadsheet).
It was suggested to try COOR MIND and use the ?MIND variable. This also
cannot be sent strait to the TITLE but one can use
SET 6 ?MIND
and write @6 to a title.
Just one of those little CHARMM idiosyncrasies I guess.....
Steve Bogusz and Dave Busath
David Busath,
I tried writing ?RAXI into a title with several of my CHARMM
versions. It works in all, so this problem may be machine or version
specific. The SHOW command will list all current substitution variables.
This is useful in debugging such a problem. Let us know what version
has this problem. Thanks,
Bernie Brooks
Hi,
I am interested in simulations of a given polymer in oil. any help in this regard will be greatly appreciated. Could this be d
greatly appreciated. Should I use Langevian ? if so what frictional coeff. is advisable. I have trieve e
tried using Toluene but the simulations take a long time!.
Thanking you in advance
--Mani--
my email add. is psubram@texaco.com
I am interested in studying polymer conformations in oil. I have done some studies using Toluene as a solvent but the runs take a long time. Is there some simpler way to incorporate the effect of oil ?. We have CHARMM running on a IBM600/550.
Can Langevian Dynamics be used here ?.
Thanking you in advance
--Mani--
my email add. is psubram@texaco.com
Hello - Sorry if this subject has been thrashed to death but I am new
to this mail-exploder. Does anyone have a list of refs to studies on the
effects/suitability of different non-bonded options used within such MM
packages as charmm amber MM2 etc. Nonbonded cutoffs, dielectric constant
etc.
Thanks
Nick Tomkinson
Hello All,
Does anyone out there have any references that involve CHARMM and
metals. Thank You.
BT
brian@opus.chem.psu.edu
Nick,
I think the "definative" paper on non-bonded cutoffs, at least as far as
CHARMm is concerned is:
Loncharich and Brooks, Proteins: Str., Func., and Genetics,
6:32-45 (1989).
I recall there being an earlier paper treating a similar thing with
AMBER. I can't remeber the reference, but it may be referred to in the
above papar.
Does anyone else have a "favourite" NBONDS setup ?
I hope this is of use.... Tim.
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax. (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || mitchell_t%frgen.dnet@smithkline.com U.K. |
-------------------------------------------------------------------------------
Roux, B & Karplus, M. 1991. Ion transport in a model gramicidin channel.
Structure and thermodynamics. Biophysical Journal 59:961-981.
Roux, B & Karplus, M. 1991. Ion transport in a model gramicidin channel.
Dynamics and mobility. J. Phys. Chem. 95:4856-4868.
----------------------------Original message----------------------------
Hello All,
Does anyone out there have any references that involve CHARMM and
metals. Thank You.
BT
brian@opus.chem.psu.edu
Roux, B & Karplus, M. 1991. Ion transport in a model gramicidin channel.
Structure and thermodynamics. Biophysical Journal 59:961-981.
Roux, B & Karplus, M. 1991. Ion transport in a model gramicidin channel.
Dynamics and mobility. J. Phys. Chem. 95:4856-4868.
----------------------------Original message----------------------------
Hello All,
Does anyone out there have any references that involve CHARMM and
metals. Thank You.
BT
brian@opus.chem.psu.edu
From chandra@yorvic.york.ac.uk Fri Jan 29 12:56:40 1993
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Via: uk.ac.york.yorvic; Fri, 29 Jan 1993 17:04:22 +0000
From: Chandra Verma <chandra@yorvic.york.ac.uk>
Date: Fri, 29 Jan 93 17:03:19 GMT
Message-Id: <21122.9301291703@yorvic.york.ac.uk>
To: charmm-bbs <@harvard:charmm-bbs@emperor>
Subject:
Does anyone calculate correlation functions from time series and fit
exponentials to estimate relaxation times. I would be grateful for some
tools.
thanx
From BROWNE@TCB2.UCSB.EDU Fri Jan 29 14:01:10 1993
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Date: Fri, 29 Jan 1993 10:59:22 -0800 (PST)
From: BROWNE@TCB2.UCSB.EDU (Kenneth A. Browne)
Message-Id: <930129105922.21c0011e@TCB2.UCSB.EDU>
Subject: CHARMm stack space
To: charmm-bbs
X-Vmsmail-To: SMTP%"charmm-bbs@emperor.harvard.edu"
To the gurus, users, and persons who just know more about CHARMm than I do,
I am (attempting) to run power CHARMm standalone on and SGI 4D/
340GTX. I have approximately 13000 atoms (mostly water molecules) in a
dynamics simulation of DNA. After the water file has been read in and the
overlapping water molecules deleted, the CHARMm script terminates due to a
***** LEVEL -4 WARNING FROM <ALLCHR> *****
***** Stack overflow
error. Stack limit on the SGI is currently set as unlimited (524288) as is
data limit. How do I increase my stack size in CHARMm? I know CHARMm
should be able to handle upto 30000 atoms. Thanks.
Kenneth A Browne
From ryszard@MSI.COM Fri Jan 29 14:24:45 1993
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Date: Fri, 29 Jan 1993 14:22:01 -0500
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9301291922.AA14926@hogan.MSI.COM>
To: BROWNE@TCB2.UCSB.EDU, charmm-bbs%emperor@harvard
Subject: Re: CHARMm stack space
Cc: ryszard@MSI.COM
Error message "Stack overflow" refers to the internal charmm
static array STACK. At the moment it is impossible to increase it
size. More precisely it is CSTACK (i.e. character STACK) since
error message comes from function ALLCHR.
In short it looks like a bug.
Please send bug report (including self-contained charmm script to
reproduce the problem) to MSI.
Ryszard Czerminski, MSI
From brbrooks@helix.nih.gov Fri Jan 29 15:24:15 1993
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Date: Fri, 29 Jan 93 15:22:04 -0500
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9301292022.AA01278@helix.nih.gov>
To: charmm-bbs
Nick,
In going beyond the work in
Loncharich and Brooks, Proteins: Str., Func., and Genetics,
6:32-45 (1989).
We have been evaluating several newer (and older) methods and we
have a second manuscript that is nearly ready for publication.
To summarize this work in terms of a recommendation, I propose the
following cutoffs:
RECOMMENDED:
Presented here is a suggested list of options. Where specifications are
missing, substitute the defaults (see NBONDS.DOC for details):
For atom based cutoffs:
NBONDS ATOM FSHIFT CDIE VDW VSHIFT -
CUTNB 14.0 CTOFNB 12.0 CTONNB 8.0 EPS 1.0 INBFRQ -1
or (perhaps better for longer cutoff distances, but a bit more expensive)
NBONDS ATOM FSWITCH CDIE VDW VSHIFT -
CUTNB 14.0 CTOFNB 12.0 CTONNB 8.0 EPS 1.0 INBFRQ -1
For group based cutoffs (but doesn't vectorize well):
NBONDS GROUP FSWITCH CDIE VDW VSWITCH -
CUTNB 14.0 CTOFNB 12.0 CTONNB 11.0 EPS 1.0 INBFRQ -1
The GROUP FSWITCH is better than GROUP SWITCH, but not as good as the
atom based methods (except for pure water). Also, cutting from 8-12
Angstroms does not do as well as 11-12 for GROUP FSWITCH.
Bernie Brooks
END --> chmbbs-jan93.log <---
BEGIN --> chmbbs-feb93.log <---
From tennantm1%frgen.dnet@smithkline.com Tue Feb 2 10:11:31 1993
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Date: Tue, 2 Feb 93 10:01:09 -0500
Message-Id: <9302021501.AA15289@smithkline.com>
From: tennantm1%frgen.dnet@smithkline.com (Mike Tennant. Harlow x3328)
To: "charmm-bbs%emperor@harvard.harvard.edu"%INET.dnet@smithkline.com
Cc: TENNANTM1@smithkline.com
Subject: Velocity Autocorrelation Functions
Hi,
Does anybody have a script which calculates velocity autocorrelation
functions, particulary diffusion coefficients. I ask this because I can't
get the solanal routines to work (no examples in the documentation!!).
Mike Tennant,
Smithkline Beecham,
Harlow,
Essex. UK.
Message 12:
From tennant@hau410 Wed Feb 3 04:24:15 1993
Date: Wed, 3 Feb 93 09:22:02 GMT
From: tennant@hau410.smithkline.com (Mike Tennant)
To: charmm-bbs%emperor@harvard
Subject: Velocity Autocorrelation Functions
Hi,
has anybody managed to get the solanal function in CHARMm to work.
I'm trying to calculate diffusion coefficients/velocity autocorrelation
functions using the prog, but the examples are rather limited (ie none!).
I would appreciate it if somebody could come to my rescue!
Mike Tennant
********************************************************************************
Mike Tennant,
Smithkline Beecham,
Coldharbour Road,
Harlow,
Essex. UK
Email: tennantm1@phvax.smithkline.com
********************************************************************************
From scsupham@reading.ac.uk Fri Feb 5 10:56:18 1993
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From: scsupham@reading.ac.uk
Date: Fri, 5 Feb 93 14:35:53 GMT
Message-Id: <4686.9302051435@scsscsc3>
To: charmm-bbs
Subject: Bacgrounding Charmm processes
Cc: scsupham@reading.ac.uk
Content-Type: X-sun-attachment
----------
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Dear charmm users,
When Running charmm script files in background, it would be
desirable to direct the output to a null file, which would avoid the
problem of directing output to a text window and therefore not being able
to logout of the machine. How can this be accomplished please ?
john upham
John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK.
Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet)
Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610
----------
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John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK.
Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet)
Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610
From ryszard@MSI.COM Fri Feb 5 11:21:34 1993
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From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9302051618.AA14248@hogan.MSI.COM>
To: charmm-bbs%emperor@harvard, scsupham@reading.ac.uk
Subject: Re: Bacgrounding Charmm processes
charmm < input > & /dev/null &
From bobf@MSI.COM Fri Feb 5 11:27:36 1993
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Date: Fri, 5 Feb 93 11:24:52 -0500
From: bobf@MSI.COM
Message-Id: <9302051624.AA01064@support>
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: charmm-bbs
Subject: Re: backgrounding CHARMm processes
On Feb 5, John Upham <scsupham@reading.ac.uk> wrote:
> Subject: Bacgrounding Charmm processes
> ----------
> X-Sun-Data-Type: text
> X-Sun-Data-Description: text
> X-Sun-Data-Name: text
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>
> Dear charmm users,
> When Running charmm script files in background, it would be
> desirable to direct the output to a null file, which would avoid the
> problem of directing output to a text window and therefore not being able
> to logout of the machine. How can this be accomplished please ?
>
> john upham
>-- End of excerpt from scsupham@reading.ac.uk
You don't specify the hardware platform you're using, so it's difficult to
answer the question. If it's a UNIX system, though, you ought to be able to
nohup /full/path/to/charmm22exe < input.script >& /dev/null &
If you actually want to keep the log, that's easier (and this should work on
any platform): Just put
open write card unit 7 name CHARMM.LOG
outu 7
near the beginning of the script.
Regards,
Bob Funchess
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From @surrey.ac.uk,@central.surrey.ac.uk:chs1nt@surrey.ac.uk Fri Feb 5 14:31:55 1993
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From: Dr Nicholas P Tomkinson <chs1nt@surrey.ac.uk>
Message-Id: <9302051637.AA05467@central.surrey.ac.uk>
Subject: background charmm
To: charmm-bbs <@harvard:charmm-bbs@emperor>
Date: Fri, 5 Feb 93 16:37:39 GMT
Mailer: Elm [revision: 66.25]
Dear John,
When I run charmm in background I use the following
command line
charmm < file.inp > waste &
this redirects the output to a file called waste. You can use
/dev/null instead which is just a wastebasket but sometimes there are
informative errors that dont appear in the LOG file but
in the waste file.
Nick Tomkinson
From chandra@yorvic.york.ac.uk Fri Feb 5 15:01:49 1993
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From: Chandra Verma <chandra@yorvic.york.ac.uk>
Date: Fri, 5 Feb 93 16:18:37 GMT
Message-Id: <11441.9302051618@yorvic.york.ac.uk>
To: charmm-bbs
Subject: Mike
Hi Mike
You do not necessarily have to use the vel acf from solanal to calculate transport coefficient D. You can can estimate it using Einstein relation
D = 1/6 { slope of the <r(t) - r(0)>2 with respect to time plot}
where r(t) is the molecule position - you do not need solanal routines
but can calculate r(t) using correl "name" atom r etc
(ref Alan & Tiddlseley - pg 60)
From KLIMKOWSKI_V_JOE@INET.D48.LILLY.COM Mon Feb 8 09:30:21 1993
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Date: 08 Feb 1993 09:27:31 -0500 (EST)
From: Joe Klimkowski <KLIMKOWSKI_V_JOE@LILLY.COM>
Subject: Redirection of charmm output
To: charmm-bbs
Message-Id: <01GUH2138OMA8WZHPA@INET.D48.LILLY.COM>
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Regarding redirecting the output from a background CHARMM job, rather than
sending the whole output to /dev/null I find it more useful to redirect only
extensive sections that may not be of any use. For instance during heating
stage of dynamics, extensive solvation of an active site (several
reapplications to insure the correct density), solvation of each residue of a
protein, or when collecting coordinate sets during dynamics using a very small
nsavc (i.e. 1 - 10, can result in a huge logfile). Alternatively, one can also
redirect the output to other files. This may be useful if you are processing
several different conformations (or even different systems) during the same
run. Below is a input file that demonstrates these ideas:
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
* test Output redirection
* Polyalanine, 20 mer
* Selectively redirect sections of the output to null unit
* Alternatively redirect sections of the output to other files
*
! Define default output unit and file
open write card unit 7 name "LFILE.LOG"
outu 7
! Redisplay banner and title for insertion into output file
banner
title
* test Output redirection
* Polyalanine, 20 mer
* Selectively redirect sections of the output to null unit
* Alternatively redirect sections of the output to other files
*
bomblev -2
wrnlev 0
prnlev 5
! define default and alternate logfile names to reinsert later
set 1 LFILE
set 2 LFILE2
! read rtf and parameter files
open read file unit 21 name "$CHM_DATA/AMINO.BIN"
read rtf file unit 21
close unit 21
open read file unit 21 name "$CHM_DATA/PARM.BIN"
read param file unit 21
close unit 21
! read sequence
read sequ card
* poly ala sequence
*
20
ala ala ala ala ala ala ala ala ala ala
ala ala ala ala ala ala ala ala ala ala
! create the psf and ic table
gene pala setup warn
! construct coordinates
ic param
ic seed 2 n 2 ca 2 c
ic build
! get initial energy
ener
! Good idea to insert title (or comments) to remind yourself what
! parts of output are being redirected and to where
title
* Polyalanine, 20 mer
* 10 steps sd mini
* logfile redirected to null unit
* will reappend to current log file after minimization
*
! HERE IS THE REDIRECTION TO THE NULL UNIT
close unit 7
open write card unit 7 name "/dev/null"
! 10 steps SD
mini sd nstep 10 nprint 1
! close null unit and reappend to default logfile
close unit 7
open append card unit 7 name "@1.LOG"
! Evaluate energy of minimized structure.
ener
! Redirect output to different file
title
* Polyalaine, 20 mer
* Second minimization, 10 steps further sd minimization
* logfile redirected to alternate file
* will reappend to current log file after second minimization
*
! HERE IS THE REDIRECTION TO alternate file
close unit 7
open write card unit 7 name "@2.LOG"
! 10 steps further SD
mini sd nstep 10 nprint 1
! close alternate file and reappend to default logfile
close unit 7
open append card unit 7 name "@1.LOG"
! Evaluate energy of final minimized structure.
ener
stop
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Joe K
klimkowski_v_joe@lilly.com
V. J. Klimkowski
Eli Lilly and Company
Indianapolis, IN 46285
From: KLIMKOWSKI V JOE (MCVAX0::RX80796)
To: VMS MAIL ADDRESSEE (IN::"charmm-bbs@emperor.harvard.edu")
cc: KLIMKOWSKI V JOE (MCVAX0::RX80796)
From brian@opus.chem.psu.edu Tue Feb 9 13:12:49 1993
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Date: Tue, 9 Feb 93 13:06:45 -0500
From: brian@opus.chem.psu.edu (Brian J. Toleno)
Message-Id: <9302091806.AA17177@opus.chem.psu.edu>
To: charmm-bbs%emperor@harvard
Subject: Parameter files and Dictionaries
I am having problems figuring out exactly how to create a parmeter file and/or
a dictonary file so I can use metals like Ti, V, Cr, etc. in a non-organic
setting. Any suggestions, hints, etc would be appreciated. Thanks in advance.
Brian Toleno
brian@opus.chem.psu.edu
From becky@MSI.COM Wed Feb 10 10:58:31 1993
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Date: Wed, 10 Feb 1993 10:55:42 -0500
From: becky@MSI.COM (Becky Rone X 276)
Message-Id: <9302101555.AA20981@franz.MSI.COM>
To: brian@opus.chem.psu.edu, charmm-bbs%emperor@harvard
Subject: Re: Parameter files and Dictionaries
If you need a QUANTA dictionary file for your molecules to run in CHARMm,
I have an awk script which will make *.dic files from RTFs.
In addition, QUANTA 3.3 has a limited set of CHARMm parameters for these
metals.
From david@einstein.ups.circe.fr Wed Feb 10 11:31:49 1993
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Date: Thu, 11 Feb 93 00:11:29 GMT
From: david@einstein.ups.circe.fr (perahia)
Message-Id: <9302110011.AA11762@einstein.ups.circe.fr>
To: charmm-bbs
Subject: plt2 program
Does anyone have the plt2 plotting program that can be
run on sgi workstations.
Thanks.
David PERAHIA
e-mail: david@einstein.ups.circe.fr
Lab. d'Enzymologie Physico-Chimique et Moleculaire
Universite Paris-Sud, Bat 430
91405 Orsay, FRANCE
From dchin Wed Feb 10 12:18:18 1993
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Date: Wed, 10 Feb 93 12:18:18 -0500
From: dchin (Donovan Chin)
Message-Id: <9302101718.AA04112@emperor.harvard.edu>
To: charmm-bbs
Subject: Torsions around 180
Charmm uses a 0 to 180 and 0 to -180 scale for angles. When torsions
fluctuate about 180, the average value is not representative of the
true (say the average is 180 deg.) value. Consequently calulations in
charmm that involve this average (ie correlation functions of dihedral
fluctuations) are off.
Question: If there a way to set the angle scale to 0-to-360? or any other
work-arounds in charmm (mainly for use in CORREL)?
regards, Donovan
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Ph.d Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From Leif.Laaksonen@csc.fi Thu Feb 11 02:54:48 1993
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Date: Thu, 11 Feb 1993 09:52:32 +0200
Message-Id: <199302110752.AA07173@csc.fi>
To: amber@cgl.ucsf.edu, charmm-bbs, gromos@igc.ethz.ch, chemistry@ccl.net
From: Leif.Laaksonen@csc.fi
Subject: SCARECROW Computing Presents
SCARECROW is a program for the analysis of MD trajectories. It has been
published in the J. Mol. Graph. 10 (1992) 33. In fact the program is much
more than just a MD analysis package. The package also contains:
(1) The ICON8 extended Huckel program modified to eat 1000 atoms. There
is an interface from SCARECROW to ICON8. The ICON8 program can
generate the input to an electrostatic potential program (VSS).
(2) The electrostatic potentiall program VSS. This is a c-code version
of the old VSS program. The out put from VSS can be displayed with
SCARECROW
(3) A probe surface program to generate Connolly type of surfaces.
(4) A program to generate orbitals or electron density data from orbitals
generated with ICON8.
SCARECROW is now able to read several different types of coordinate
files like the CHARMM, INSIGHT, PDB and several other types of files.
Trajectory analysis can be done for CHARMM, DISCOVER, YASP, MUMOD,
GROMOS, and AMBER binary trajectories, and very soon also for
HyperChem. Some of the goodies are only available for CHARMM users.
New features in SCARECROW are the possibility to calculate radial
distribution functions, power spectrum for main component analysis
of time series and a possibility to calculate diffusion coefficients
and much more. There is a very crude 2D display facility but the
data can always be exported to your favourite plotting package.
SCARECROW has a graphics interface and runs now only on Silicon
Graphics Machines. On SGI machines it's also possible to run
SCARECROW without graphics. I don't have any plans to port
the stuff to other platforms, sorry.
If you are interested to get more information about SCARECROW
please feel free to get in touch. I have so far been distributing
the program for free, if somebody makes money out of it I want
to get my share.
Cheers,
-leif laaksonen
---------------------------------------------------------
Leif.Laaksonen@csc.fi
Center for Scientific Computing
P.O. Box 405
FIN-02101 Espoo
FINLAND
Phone: 358 0 4572378
Telefax: 358 0 4572302
Voice Mail: 358 486257407
"In every job to be done
there is an element of fun"
Mary Poppins
---------------------------------------------------------
From arne@mango.mef.ki.se Mon Feb 15 03:50:58 1993
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id AA00964; Mon, 15 Feb 93 03:50:58 -0500
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id AA18268; Mon, 15 Feb 93 09:49:09 GMT
From: arne@mango.mef.ki.se (Arne Elofsson)
Message-Id: <9302150949.AA18268@mango.mef.ki.se>
To: david@einstein.ups.circe.fr (perahia)
Cc: charmm-bbs%emperor@harvard, arne@mango.mef.ki.se
Subject: Re: plt2 program
In-Reply-To: (Your message of Thu, 11 Feb 93 00:11:29 GMT.)
<9302110011.AA11762@einstein.ups.circe.fr>
Date: Mon, 15 Feb 93 09:49:09 +0000
I know that it exists.
I think I can find it but I do not
knoe if I am allowed to give it away
Please contact :
c Copyright 1984 - David J. States
c National Magnet Laboratory, MIT
c Cambridge, MA 02139
SOrry I do not have an email adress.
arne
From jpoole@oucsace.cs.ohiou.edu Wed Feb 17 16:43:58 1993
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id AA23843; Wed, 17 Feb 93 16:41:33 EST
Date: Wed, 17 Feb 93 16:41:33 EST
From: James Poole <jpoole@oucsace.cs.ohiou.edu>
Message-Id: <9302172141.AA23843@oucsace.cs.ohiou.edu>
To: charmm-bbs
Subject: Using Partial Coordinates
Hello Fellow Computational Chemistry Mailing List Readers,
I have a small problem setting up a protein structure in CHARMM that someone
here may know the answer.
I am working on a model of a coiled-coil protein. I have the alpha helices
defined as I need them but I am having difficulty getting the left-handed
super-coiling of the two alpha helices. The last approach that I have used seems
to be the most reasonable method for getting the backbone dihedrals defined
to give the required coiled-coil. This approach is to use the C-alpha coordinates
for tropomyosin from the Brookhaven PDB as a template. What I attempted was to
read in the sequence of my protein into CHARMM and set up the internal coordinates
from the parameter files like normal. The next step was to read in the coordinates
of the Tm C-alphas from a file modified to have the correct residue names and
numbers and then build the coordinates, energy minimize with constraints, and
dock the two helices. The snag is that the read-in coordinates are overwritten
when the remaining coordinates are build (unexpected based on the manuals).
What I am interested in knowing is has anyone used partial defined coordinates and
then built the remaining ones succesfully and if so will you share your wisdom.
I have also sent this to the CHARMM mail-exploder and have a call into MSI, but
this seems to be the best resource for practical experience.
Thanks in advance,
Jim Poole, (614) 593-1744 voice
Ohio University, (614) 593-llll fax
Dept. of Chemistry jim@quanta.phy.ohiou.edu or jpoole@oucsace.cs.ohiou.edu
---- begin sample charmm code ----
>
> start of charmm code omitted
>
> GENE HLXA SETU
>
> IC PARA
> OPEN READ CARD UNIT 14 NAME INPUT.CRD
> READ COOR CARD UNIT 14
> CLOSE UNIT 14
> IC BUILD
>
> remainder of code omitted
>
From bobf@MSI.COM Wed Feb 17 17:28:52 1993
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id AA02234; Wed, 17 Feb 93 17:28:52 -0500
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id AA20010; Wed, 17 Feb 93 17:23:38 EST
Received: by support (920330.SGI/911001.SGI)
for charmm-bbs@emperor.harvard.edu id AA00659; Wed, 17 Feb 93 17:25:42 -0500
Date: Wed, 17 Feb 93 17:25:42 -0500
From: bobf@MSI.COM
Message-Id: <9302172225.AA00659@support>
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: jim@quanta.phy.ohiou.edu, charmm-bbs
Subject: setting up coordinates from Calpha positions
Here's a script that does this for the 1CBP protein; it should be fairly easy
to modify it for other PDB files. The first residue is 1CBP is numbered "11"
in the file, so the 11's in the script should be changed to be appropriate for
the pdb file you're trying to read in.
Bob Funchess
------cut here -------
* Script file produced by QUANTA
*
! Startup script for CHARMm
!
UPPER ! case for files to write
banner
bomblevel -2
wrnlev 0
prnlev 5
open read file unit 21 name "$CHM_DATA/AMINO.BIN"
read rtf file unit 21
close unit 21
open read file unit 21 name "$CHM_DATA/PARM.BIN"
read param file unit 21
close unit 21
DELE ATOM SELECT ALL END
open read unit 21 card name "1cbp.pdb"
read sequ pdb unit 21
close unit 21
generate 1CBP setup
open read unit 21 card name "1cbp.pdb"
read coor pdb unit 21
close unit 21
coor orie norotate sele atom 1CBP 11 CA end
coor tran xdir -1 dist 1.5 sele all end
coor set xdir 1 dist 0 sele atom 1CBP 11 N end
coor set xdir 1 dist 0 sele atom 1CBP 11 C end
coor tran xdir 1 ydir 2 dist 2.5 sele atom 1CBP 11 C end
coor init sele .not. -
(atom 1CBP 11 N .or. atom 1CBP 11 C .or. atom 1CBP * CA) end
ic param
ic build
hbuild
open write unit 22 card name "1cbp.CRD"
coor write card unit 22
* Title
*
close unit 22
STOP
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From brian@opus.chem.psu.edu Thu Feb 25 15:04:20 1993
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Date: Thu, 25 Feb 1993 15:03:07 -0500
From: brian@opus.chem.psu.edu (Brian J. Toleno)
Message-Id: <9302252003.AA11867@opus.chem.psu.edu>
To: CHARMM-BBS%emperor@harvard
I was wondering if anyone out there was running QUANTA 3.2.3 CHARMm 21.3
on the new AIX version (3.3 ?). The reason I am asking is that since we
updated we can no longer run quanta we get the error message:
Could not load program /usr/local/quanta/exec/quanta.exe
Could not load library libgl.a[shr.o]
Error was: No such file or directory
Has anyone seen this error before or have any ideas. We have restored all the
directories exactly as they were previously, the only thing that has been
changed is the operating system.
Thanks
BT
From bobf@MSI.COM Thu Feb 25 15:48:24 1993
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id AA10500; Thu, 25 Feb 93 15:48:24 -0500
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for charmm-bbs@emperor.harvard.edu id AA02035; Thu, 25 Feb 93 15:44:45 -0500
Date: Thu, 25 Feb 93 15:44:45 -0500
From: bobf@MSI.COM
Message-Id: <9302252044.AA02035@support>
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: charmm-bbs
Subject: Re: Brian J. Toleno's question
For those members of the CHARMm community who may be using Quanta and seeing
problems similar to this, the most likely answer is that the GL was not loaded
for some reason or other. GL is the Graphics Library, and unless it's present
on the system many of the Quanta graphics calls will fail. Check the software
configuration and make sure that all the necessary graphics libraries are in
fact on the system.
Bob Funchess
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From W.P.vanHoorn@ct.utwente.nl Mon Mar 1 11:51:47 1993
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for @utct.ct.utwente.nl:charmm-bbs@emperor.harvard.edu id AA07962; Mon, 1 Mar 93 17:51:08 GMT
Date: Mon, 1 Mar 93 17:51:08 GMT
From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9303011751.AA07962@utctu2>
To: charmm-bbs
Subject: Enter CHARMm Newsgroup
Dear Sir/Madam,
Can you enter to the CHARMm newsgroup?
Thanks,
W.P. van Hoorn
Organic Chemistry Department
University of Twente
P.O. Box 217
7500 AE Esnschede
The Netherlands
wphoorn@ct.utwente.nl
END --> chmbbs-feb93.log <---
BEGIN --> chmbbs-mar93.log <---
From eldbjorg@chem.uit.no Wed Mar 3 05:25:35 1993
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id <23454-0@ppenoni.uit.no>; Wed, 3 Mar 1993 11:07:52 +0000
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by benoni.uit.no (5.65+IDA/Babel-1.15/ABaa-1.2/Ultrix)
id AAbenoni23450; Wed, 3 Mar 1993 11:07:50 +0100
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Wed, 3 Mar 93 10:10:41 GMT
Date: Wed, 3 Mar 93 10:10:41 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9303031010.AA08948@trypsin.chem.uit.no>
To: charmm-bbs
Subject: COOR DYNA
COOR DYNA calculates average coordinates and isotropic fluctuations from
a trajectory file. Can someone tell me if there exist an equation for
the calculation of isotropic fluctuation, and is it designated as
Angstrom or the square of Angstrom?
What is the relation of this value to X-ray isotropic B-value --
multiply with 26 !? ...........
Thanks in advance,
Elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From kuczera@tedybr.chem.ukans.edu Wed Mar 3 10:29:21 1993
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Date: Wed, 3 Mar 1993 09:24:29 -0600
From: kuczera@tedybr.chem.ukans.edu
Message-Id: <9303031524.AA18477@tedybr.chem.ukans.edu>
To: charmm-bbs%emperor@harvard
Hi,
The values stored in the WMAIN array (fourth column of numbers
in the coordinate file) are root mean square position fluctuations
for each atom i:
(rms fluct)i = SQRT(<dRi**2>)
dRi**2 = (xi - <xi>)**2 + (yi - <yi>)**2 + (zi - <zi>)**2
where xi,yi,zi are cartesian coordinates of atom i,
x - <x>, ...etc. are the displacements from the average positions,
<...> denotes averaging over the trajectory
The units of x,y,z and the rms fluctuations are thus A.
see SUBROUTINE AVECOR in module dynanal.src for details.
Crystallographic isotropic B factors are proportional to the mean square
position fluctuations,
B = 8*(pi**2)*<(x - <x>)**2> = 8*(pi**2)*<dR**2>/3 = 26.3*<dR**2>
the last equation, as some textbooks say, can be used to estimate pi ...
Krzysztof Kuczera
Department of Chemistry
University of Kansas
2010 Malott Hall
Lawrence, KS 66045
tel: (913) 864-5060 (my office) or 864-4670 (Chemistry office)
fax: (913) 864-5396
e-mail: kuczera@tedybr.chem.ukans.edu
chant: rock-chalk-jayhawk
warning: careful with that last sentence
From kuczera@tedybr.chem.ukans.edu Wed Mar 3 10:47:19 1993
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Date: Wed, 3 Mar 1993 09:42:21 -0600
From: kuczera@tedybr.chem.ukans.edu
Message-Id: <9303031542.AA16945@tedybr.chem.ukans.edu>
To: charmm-bbs%emperor@harvard
Hi,
Here is some information on:
Coordinate fluctutations from COOR DYNA
The values stored in the WMAIN array (fourth column of numbers
in the coordinate file) are root mean square position fluctuations
for each atom i:
(rms fluct)i = SQRT(<dRi**2>)
dRi**2 = (xi - <xi>)**2 + (yi - <yi>)**2 + (zi - <zi>)**2
where xi,yi,zi are cartesian coordinates of atom i,
x - <x>, ...etc. are the displacements from the average positions,
<...> denotes averaging over the trajectory
The units of x,y,z and the rms fluctuations are thus A.
see SUBROUTINE AVECOR in module dynanal.src for details.
Crystallographic isotropic B factors are proportional to the mean square
position fluctuations,
B = 8*(pi**2)*<(x - <x>)**2> = 8*(pi**2)*<dR**2>/3 = 26.3*<dR**2>
the last equation, as some textbooks say, can be used to estimate pi ...
Krzysztof Kuczera
Department of Chemistry
University of Kansas
2010 Malott Hall
Lawrence, KS 66045
tel: (913) 864-5060 (my office) or 864-4670 (Chemistry office)
fax: (913) 864-5396
e-mail: kuczera@tedybr.chem.ukans.edu
chant: rock-chalk-jayhawk
warning: careful with that last sentence
From @surrey.ac.uk,@central.surrey.ac.uk:chs1nt@surrey.ac.uk Wed Mar 3 13:47:57 1993
Received: from sun2.nsfnet-relay.ac.uk by emperor.harvard.edu via SMTP (920110.SGI/911001.SGI) id AA15527; Wed, 3 Mar 93 13:47:57 -0500
Via: uk.ac.surrey; Wed, 3 Mar 1993 14:21:09 +0000
Via: central.surrey.ac.uk; Wed, 3 Mar 93 14:20:30 GMT
Received: by central.surrey.ac.uk (16.6/16.2) id AA23190;
Wed, 3 Mar 93 14:20:29 GMT
Date: Wed, 3 Mar 93 14:20:29 GMT
From: Dr Nicholas P Tomkinson <chs1nt@surrey.ac.uk>
Message-Id: <9303031420.AA23190@central.surrey.ac.uk>
Apparently-To: charmm-bbs
Does anyone know of a simple (free) script for grgenerating an RTF files
from a structure without having to use QUANTA? Similarly, does anyone
have a script/scripts for converting betwwen files for AMBER/CHARMMM/DISCOVER?
Ceers
Nick Tomkinson
From EDBRIDGES@MERLIN.NLU.EDU Wed Mar 3 15:23:22 1993
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Date: Wed, 3 Mar 1993 14:24:10 -0600 (CST)
From: EDBRIDGES@MERLIN.NLU.EDU (Steve Bridges, Health and Human Performance)
Message-Id: <930303142410.5bb2@MERLIN.NLU.EDU>
Subject: unsubscribe
To: charmm-bbs
X-Vmsmail-To: SMTP%"charmm-bbs@emperor.harvard.edu"
Thank you for removing me from your BBS.
FSB
From eldbjorg@chem.uit.no Wed Mar 3 15:26:07 1993
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id <27373-0@ppenoni.uit.no>; Wed, 3 Mar 1993 21:23:24 +0000
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Date: Wed, 3 Mar 93 20:26:16 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9303032026.AA09492@trypsin.chem.uit.no>
To: charmm-bbs
Subject: COOR DYNA and ISOTROPIC B-factor
Thanks to Kuczera!
Excellent answer to my question.
-elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From tennant@hau410.uk.smithkline.com Thu Mar 4 05:48:48 1993
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for charmm-bbs%emperor@harvard.harvard.edu id AA09659; Thu, 4 Mar 93 10:48:58 GMT
Date: Thu, 4 Mar 93 10:48:58 GMT
From: tennant@hau410.uk.smithkline.com (Mike Tennant)
Message-Id: <9303041048.AA09659@hau410.uk.smithkline.com>
To: charmm-bbs%emperor@harvard
Subject: Reaction Fields and Membrane Simulations
Hi,
I'm trying to get some info about the reaction field calcs in CHARMm.
Specifically, can it be used to simulate a non-spherical field, ie around
a protein. The reaon I am interested in this is that I am trying to
simulate a receptor in a membrane using various models eg lipid, lipid+solvent,
LD, MD etc. Does anybody have experience in calcs of this type.
Also , any examples of the RXN field keyword in action would be
most appreciated
Mike Tennant
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Coldharbour Rd |
| | |___ \\|_| | || Harlow |
| \____ \ | _ < || Essex |
| ___| | | |_| | || CM19 5AD |
| \_____/ |____/ || England |
| || |
|_____________________________________________________________________________|
| Mike Tennant |
| Harlow (0279) 622000x3328 |
| Email: tennantm1@smithkline.com |
| Email: smithkline.com!hau410.uk.smithkline.com!tennant |
-------------------------------------------------------------------------------
From W.P.vanHoorn@ct.utwente.nl Thu Mar 4 10:49:18 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9303041648.AA06640@utctu2>
Subject: Printing of *.doc files
To: charmm-bbs ( CHARMm BBS)
Date: Thu, 4 Mar 1993 16:47:54 +0000 (WET)
X-Mailer: ELM [version 2.4 PL5]
Content-Type: text
Content-Length: 875
Hi CHARMm users,
In the directory $CHM_DATA/doc (= /usr/msi/quanta3.3/data/doc on Silicon
Graphics) I find files with all kind of usefull information. What is the
status of these files, some information in them seems not correct?
For instantce the command 'SPECIfy' in the file miscom.doc is not recognized
by CHARMm (vs 22.0).
How can I print these files, they are in ASCII, but contain some
format commands I do not know.
Thanks,
----------------------------------------------------------------------
Willem Paul van Hoorn (ir.)
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (NL)53-892955
P.O. Box 217 (NL)53-892980
7500 AE Enschede, The Netherlands fax : (NL)53-356024
----------------------------------------------------------------------
From ryszard@MSI.COM Thu Mar 4 12:21:43 1993
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Date: Thu, 4 Mar 1993 12:18:39 -0500
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9303041718.AA13580@hogan.MSI.COM>
To: W.P.vanHoorn@ct.utwente.nl, charmm-bbs%emperor@harvard
Subject: Re: Printing of *.doc files
*.doc files contain on-line charmm documentation,
which (at least in principle) should be fully
synchronized with the status of the code.
If you find problems as described in your note
please report them so we can correct them.
How to print neatly *.doc files I am not quite sure...
Ryszard Czerminski, MSI
From jarrinm@woods.ulowell.edu Thu Mar 4 13:44:07 1993
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Date: Thu, 04 Mar 1993 13:41:34 EST
From: jarrinm@woods.ulowell.edu
To: charmm-bbs%emperor@harvard
Message-Id: <0096901B.2F9F8AA0.15739@woods.ulowell.edu>
Subject: RE: *.doc files
I do not believe all *.doc files are updated, but only those that
have listed the update dates on the beggining of each *.doc file.
More important, not all *.doc files contain a line that says "c22doc".
Mario Jarrin
From jarrinm@woods.ulowell.edu Thu Mar 4 15:10:04 1993
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Date: Thu, 04 Mar 1993 15:07:20 EST
From: jarrinm@woods.ulowell.edu
To: charmm-bbs%emperor@harvard.edu
Message-Id: <00969027.2ADDC660.15995@woods.ulowell.edu>
Subject: TEST
TEST
From arne@mango.mef.ki.se Fri Mar 5 03:38:11 1993
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Date: Fri, 5 Mar 93 09:36:29 GMT
From: arne@mango.mef.ki.se (Arne Elofsson)
Message-Id: <9303050936.AA12215@mango.mef.ki.se>
To: charmm-bbs, hotline@msi.com
Subject: Quanta license code.
Dear netters and people at MSI.
I have now during two weeks been
trying to get quanta3.2 running again.
I have an IBM/RS6000 running aix3.1.5
and the problems started when I changed
the IP number of the (damned) machine.
After that it seems like the licencemanager
did not start again. It does not complain
when I start it but the licence manager is
not running. I guess that the problem
is due to some nameserving business, but
everything else works fine, the machine knows
itself etc ....
DO ANYONE HAVE ANY SUGGESTIONS ?
arne
From hotline@MSI.COM Fri Mar 5 09:40:47 1993
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Date: Fri, 5 Mar 93 09:37:13 -0500
From: hotline@MSI.COM
Message-Id: <9303051437.AA04261@support>
Organization: Molecular Simulations Inc.
Phone: (617) 229-8872
Fax: (617) 229-9092
To: charmm-bbs
Subject: Quanta3.3 license installation for Arne Elofsson
Arne,
Since we have made several attempts to get Quanta running on your IBM machine, the
best thing to try is to make sure that you can telnet to your own machine using
the proper name. This will insure that the network is properly configured.
Starting the license manager will generate a license.log file in /etc/ directory.
What is contained in this file? The final solution if all else fails is to
delete the license.dat file and to reinstall the license.
If you are still having problems please contact MSI Scientific Support.
Nick Reynolds
--
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* 16 New England Executive Park *
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From ammon@chema.umd.edu Mon Mar 8 15:32:01 1993
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Date: Mon, 08 Mar 1993 15:33:35 EST
From: ammon@chema.umd.edu
To: charmm-bbs%emperor@harvard
Message-Id: <0096934F.7FC959C0.2660@chema.umd.edu>
Subject: Ewald parameters
To MSI QUANTA/CHARMm and stand-alone CHARMM users....
HELP! I am using the QUANTA Crystal Builder option to set
up the appropriate CHARM commands to perform crystal lattice refinement
(energy minization). In order to have the inter-molecular electrostatic terms
handled properly in the calculations, it is necessary to turn-on the EWALD
switch located in the CHARMm Update Parameters palette. Part of the turn-on
presumably involves setting values for three variables called "kappa",
"nvec" and "length" (all initally 0). Unfortunately, there is no
documentation on what these are and/or should be set to and there are no
CHARM parameters with these names. I've spoken to the MSI folks in Mass.
about this, but memories being what they are, they cannot remember what
the parameters are supposed to be or a literature reference.
Can someone out there please lend a hand. PLEASE do not suggest that I
go back to Ewald's 1921 original paper.
Thanks,
Herman Ammon
Dept. of Chemistry & Biochemistry
Univ. of Maryland
College Park, MD 20742
phone = 301-405-1824
FAX = 301-314-9121
From jim@quanta.phy.ohiou.edu Thu Mar 11 23:55:10 1993
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Date: Fri, 12 Mar 93 04:51:15 GMT
From: jim@quanta.phy.ohiou.edu (Jim Poole)
Message-Id: <9303120451.AA00720@quanta.phy.ohiou.edu>
To: CHEMISTRY@ccl.net, charmm-bbs
Subject: source for CONGEN
Does anyone in the CHARMm or Computanional Chemistry list have any
information about the program CONGEN by Bruccoleri and Karplus
(Biopolymers 26, 137-168 (1987))?
Is this program available from any of commercial venders, QCPE,
anonymous FTP, or the authors?
Can anyone who may have used it give estimates of cpu time needed to
build sidechains for 10 residues, 25 residues, or 100 residues(gasp!)?
I have read the appropriate references and I am very interested in this
program.
Thanks in advance,
Jim Poole,
Ohio University,
Dept. of Chemistry
phone (614) 593-1744
fax (614) 593-0l48
email jim@quanta.phy.ohiou.edu or jpoole@oucsace.cs.ohiou.edu
From robert@sg1.oc.wau.nl Fri Mar 12 03:48:51 1993
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Date: Fri, 12 Mar 93 09:44:19 GMT
From: robert@sg1.oc.wau.nl (Robert Schrijvers)
Message-Id: <9303120944.AA06167@Sg1.OC.wau.nl>
To: charmm-bbs%emperor@harvard
Subject: usercharmm
Hi,
Who could help me solve a F77 linking problem?
I tried to make my own charmm version by linking the charmm object files
Every time I try to do this I encounter the same error message from the
linker: three procedures are not defined ie. do_fio8,do_fioi4 and do_fior4.
In my archive files there are no such procedures defined.
I am running this on a Silicon Graphics personal Iris 4D25.
Thanks in advance,
Robert Schrijvers
Molecular Modeling & Design
Department of Organic Chemistry
Agricultural University Wageningen
Dreijenplein 8 6703 HB Wageningen
The Netherlands
Phone: 08370-82364
FAX:08370-84914
e-mail: robert@SG1.OC.WAU.NL
From jim@quanta.phy.ohiou.edu Fri Mar 12 14:02:28 1993
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Date: Fri, 12 Mar 93 18:58:50 GMT
From: jim@quanta.phy.ohiou.edu (Jim Poole)
Message-Id: <9303121858.AA01740@quanta.phy.ohiou.edu>
To: charmm-bbs
Subject: CONGEN found
Thanks for all the response about CONGEN. I have since spoke with
Robert Bruccoleri, the author, and I am getting the liscence in place.
Thanks again for the info.
Jim Poole
Chemistry Deptament,
Ohio University
phone (614)593-1744
fax (614)593-0148
email jim@quanta.phy.ohiou.edu or jpoole@oucsace.cs.ohiou.edu
From W.P.vanHoorn@ct.utwente.nl Fri Mar 12 17:19:05 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9303120940.AA03080@utctu2>
Subject: Re: Ewald parameters
To: charmm-bbs ( CHARMm BBS)
Date: Fri, 12 Mar 1993 09:40:44 +0000 (WET)
X-Mailer: ELM [version 2.4 PL5]
Content-Type: text
Content-Length: 688
In the file commands.doc (On silicon graphics: $CHM_DATA/doc/commands.doc)
is a reference to a file ewald.doc which unfortunately is not present. See
also my earlier question about these doc files. Does still nobody knows how
to print them?
Regards,
----------------------------------------------------------------------
Willem Paul van Hoorn (ir.)
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (NL)53-892955
P.O. Box 217 (NL)53-892980
7500 AE Enschede, The Netherlands fax : (NL)53-356024
----------------------------------------------------------------------
From jarrinm@woods.ulowell.edu Fri Mar 12 17:46:06 1993
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Date: Thu, 11 Mar 1993 14:03:24 EST
From: jarrinm@woods.ulowell.edu
To: charmm-bbs
Message-Id: <0096959E.65A85360.29668@woods.ulowell.edu>
Subject: Averages & rms fluctuatios
When doign a dynamics run is possible to ask charmm to print out
averages and rms fluctuatios of the major energy terms. This is done
by setting IPRFRQ = to a specific # of steps which dictates how
often the averages and rms are sent the output file. Is there any
way to instruct charmm to print cummulative averages and rms values?
By cummulative I mean an output every N steps which includes ALL
previous takes steps (not only of the last N steps). This occurs
during the symulation stage of a dynamics run but I would like to
obtain the same output for the equilibration stage.
I thank you in advance for your input.
Mario Jarrin
From W.P.vanHoorn@ct.utwente.nl Fri Mar 12 17:48:55 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9303121412.AA05171@utctu2>
Subject: Re: Ewald parameters
To: charmm-bbs ( CHARMm BBS)
Date: Fri, 12 Mar 1993 14:11:49 +0000 (WET)
X-Mailer: ELM [version 2.4 PL5]
Content-Type: text
Content-Length: 688
In the file commands.doc (On silicon graphics: $CHM_DATA/doc/commands.doc)
is a reference to a file ewald.doc which unfortunately is not present. See
also my earlier question about these doc files. Does still nobody knows how
to print them?
Regards,
----------------------------------------------------------------------
Willem Paul van Hoorn (ir.)
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (NL)53-892955
P.O. Box 217 (NL)53-892980
7500 AE Enschede, The Netherlands fax : (NL)53-356024
----------------------------------------------------------------------
From JARRINM%AM.mrgate@woods.ulowell.edu Thu Mar 18 17:47:17 1993
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Date: Thu, 18 Mar 1993 17:44:30 EST
From: JARRINM%AM.mrgate@woods.ulowell.edu
To: CHARMM-BBS
X-Vmsmail-To: CHARMM-BBS@EMPEROR.HARVARD.EDU
Message-Id: <00969B3D.71ABE740.10290@woods.ulowell.edu>
Subject: Periodic Boundary Conditions
From: NAME: JARRINM
TEL: N/A
ADDR: STUDENT <JARRINM@AM@WOODS>
To: charmm-bbs@emperor.harvard.edu@INTERNET
I am trying to learn to use PBC in the simulations I run. To my
dissapointment I could not find any reference to the PBOU command in the
charmm documentation that I have. Can anibody provide me (or tell me where
I could get) the information I need in order to learn about the use of
this command in charmm?
I already thank you for your help.
Mario Jarrin
Chemistry Dpt.
U. of MA at Lowell
One University Ave
Lowell, MA 01854
(508)934-3708/3541
e-mail:jarrinm@woods.ulowell.edu
From eldbjorg@chem.uit.no Thu Mar 25 05:15:32 1993
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Date: Thu, 25 Mar 93 10:08:15 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9303251008.AA02831@trypsin.chem.uit.no>
To: charmm-bbs
Subject: CDIE or RDIE; Solvation
The choice of dielectric constant:
is there a general opinion among CHARMm users that a distance
dependent dielectric constant for in vacuo conditions is history?
( I have some copies of lecture notes from CHARMm course 1990, which
recommend the use of constant dielectric for both in vacuo and aqueous
conditions).
There are many methods for solvating molecules, but which method is
recommended if you want to solvate the whole protein (i.e. not stochastic
boundary cond.) in water; box, radius, image etc..?
Is image only used for the box option?
Is there any documentation for use of SOLVATE8.STR etc.( under
msi/quanta3.3/data directory)?
Something else: Does anybody have experience with serine proteases
and the residue numbering; 184A 184, 188A 188, 221A 221. Does CHARMm
get any problem with this?
-elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From F0388913@JAGUAR.CSC.WSU.EDU Thu Mar 25 13:27:06 1993
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Date: Thu, 25 Mar 1993 10:24:03 -0800 (PST)
From: F0388913@JAGUAR.CSC.WSU.EDU (Brian W. Beck)
Message-Id: <930325102403.20605299@JAGUAR.CSC.WSU.EDU>
Subject: Making a solvent box of DMF
To: charmm-bbs%emperor@harvard
X-Vmsmail-To: SMTP%"charmm-bbs%emperor@harvard.harvard.edu"
Has anyone ever done or heard of anyone using
dimethylformamide for solvent. I know of parameters
for formamide, and for N-Methyl acetamide, but I can't
for any literature sources for equilibrium bond lengths
(ie. structure) and partial charges for DMF. I've built a
DMF and calculated the partial charges using MOPAC, but I'd
like to compare this to other work or literature precedent.
Also, I've got a question about creating novell solvent boxes
that you all can probably answer.
After minimizing what I hope is a reasonable single molecule
structure of DMF, I created a pseudo regular array of them by
replicating the DMF over a lattice that would give me a density
of 0.9487 g/ml, but I randomly oriented the DMF at each lattice
point so I wouldn't have a regular crystal of DMF.
I'm going to minimize for a few steps to get rid of bad contacts,
but I was wondering whether I should start equilibrating my box at
0 K and ramp up to 300K or should I just start at 300K since
I'm don't have regular structure to protect by ramping the temperatures.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
=========
SYMPOSIUM
=========
Simulation of Polypeptide and Protein Structure
May 3-4, 1993
A symposium to discuss research progress in the Theory CenterUs Parallel
Processing Resource for Biomedical Scientists, as well as recent advances
in computational chemistry and polypeptide modeling.
========
LOCATION
========
Sheraton Inn and Conference Center
One Sheraton Drive
Ithaca, New York 14850
==================
PRELIMINARY AGENDA
==================
Malvin H. Kalos
Director, Cornell Theory Center
Welcome & Overview of the Parallel
Processing Resource for Biomedical Scientists
David Shalloway
Biochemistry, Cornell University
Effective Energy Simulating Annealing for Molecular Structure
Prediction
Harold Scheraga
Chemistry, Cornell University
The Multiple-minima Problem in
Protein Folding
Peter Kollman
University of California/San Francisco
Molecular Dynamics and Free Energy
Calculations of Protein
George Nemethy
Biomathematical Sciences/Mt. Sinai Medical Center
The Structure and Assembly of Collagen
Daniel Ripoll/Richard Gillilan
Cornell Theory Center
Simulation and Visualization of
Acetylcholinesterase Electrostatics
Klaus Schulten
Physics, University of Illinois
Urbana-Champaign
Large Scale Simulations of
Protein-Membrane Systems
John Brady
Food Science, Cornell University
Molecular Dynamics Simulations of
Carbohydrates
Andrew McCammon
Chemistry, University of Houston
Computer-aided Molecular Design
Chani Pangali
Kendall Square Research Corporation
Computational Chemistry on the KSR1
Jan Hermans
Professor, Biophysics University of North Carolina/Chapel Hill
Molecular Dynamics Studies of Peptide
Conformational Equilibrium
Dr. Dzung Nguyen, Ph.d
Scientist, Biosym Technologies, Inc.
Molecular Dynamics Study of the Structure and Dynamics of Proteins in
a Crystalline Lonic Environment
==============
POSTER SESSION
==============
To apply for a poster session and/or video theatre presentation, please send
abstract of research to cal@tc.cornell.edu by March 30, 1993.
========
WORKSHOP
========
In conjunction with the symposium, the Theory Center will conduct,
during May 5-7, a training workshop on using the KSR1 parallel
computer. A fee will be charged for the training workshop. Registration
available separately.
==============
ACCOMMODATIONS
==============
Two local hotels have set aside rooms for the nights of May 3-4. Please
make your reservations directly with the hotel and mention that you are
coming for the Simulation of Polypeptide and Protein Structure
symposium. Reservations must be made by April 12 to assure room
availability.
Sheraton Inn
One Sheraton Drive
Ithaca, NY 14850
607-257-2000 or 1-800-257-6992
607-257-3998 (fax)
Rates start at $62
Holiday Inn
2310 North Triphammer Road
Ithaca, NY 14850
607-257-3100 or 1-800-465-4329
607-257-4425 (fax)
Rates start at $60
=================
REGISTRATION FORM
=================
Return this part only, by April 5:
Symposium on Simulation of Polypeptide
and Protein Structure
May 3-4, 1993
Sheraton Inn and Conference Center, Ithaca, NY
Name: __
Title: __
Organization: __
Address: __
City/State/Zip/Country: __
Phone/Fax: __
Email: __
Special dietary requirements:
Kosher__
Vegetarian__
Other ________________________________________
Return completed form to:
(deadline April 5, 1993)
Donna Smith, Conference Coordinator
422 Theory Center
Cornell University
Ithaca, NY 14853
607-254-8686; 607-254-8888 (fax)
donna@tc.cornell.edu
From dchin Mon Mar 29 13:24:03 1993
Received: by emperor.harvard.edu (920110.SGI/911001.SGI)
id AA10555; Mon, 29 Mar 93 13:24:03 -0500
Date: Mon, 29 Mar 93 13:24:03 -0500
From: dchin (Donovan Chin)
Message-Id: <9303291824.AA10555@emperor.harvard.edu>
To: charmm-bbs
Subject: Parallel Processing Symposium
I am posting this from:
From jeanne@TC.Cornell.EDU Mon Mar 29 13:00:24 1993
Date: Mon, 29 Mar 1993 12:57:12 -0500
From: "Jeanne C. Miller" <jeanne@TC.Cornell.EDU>
To: amber@cgl.ucsf.edu, charmm-bbs-sysop, chemistry@ccl.net,
dibug@comp.bioz.unibas.ch, gromos@igc.ethz.ch, hyperchem@autodesk.com,
mmodinfo@uoft02.utoledo.edu, spasms-users@cgl.ucsf.edu,
sybylreq@quant.chem.rpi.edu
Subject: KSR Symposium Announcement
=========
SYMPOSIUM
=========
Simulation of Polypeptide and Protein Structure
May 3-4, 1993
A symposium to discuss research progress in the Theory CenterUs Parallel
Processing Resource for Biomedical Scientists, as well as recent advances
in computational chemistry and polypeptide modeling.
========
LOCATION
========
Sheraton Inn and Conference Center
One Sheraton Drive
Ithaca, New York 14850
==================
PRELIMINARY AGENDA
==================
Malvin H. Kalos
Director, Cornell Theory Center
Welcome & Overview of the Parallel
Processing Resource for Biomedical Scientists
David Shalloway
Biochemistry, Cornell University
Effective Energy Simulating Annealing for Molecular Structure
Prediction
Harold Scheraga
Chemistry, Cornell University
The Multiple-minima Problem in
Protein Folding
Peter Kollman
University of California/San Francisco
Molecular Dynamics and Free Energy
Calculations of Protein
George Nemethy
Biomathematical Sciences/Mt. Sinai Medical Center
The Structure and Assembly of Collagen
Daniel Ripoll/Richard Gillilan
Cornell Theory Center
Simulation and Visualization of
Acetylcholinesterase Electrostatics
Klaus Schulten
Physics, University of Illinois
Urbana-Champaign
Large Scale Simulations of
Protein-Membrane Systems
John Brady
Food Science, Cornell University
Molecular Dynamics Simulations of
Carbohydrates
Andrew McCammon
Chemistry, University of Houston
Computer-aided Molecular Design
Chani Pangali
Kendall Square Research Corporation
Computational Chemistry on the KSR1
Jan Hermans
Professor, Biophysics University of North Carolina/Chapel Hill
Molecular Dynamics Studies of Peptide
Conformational Equilibrium
Dr. Dzung Nguyen, Ph.d
Scientist, Biosym Technologies, Inc.
Molecular Dynamics Study of the Structure and Dynamics of Proteins in
a Crystalline Lonic Environment
==============
POSTER SESSION
==============
To apply for a poster session and/or video theatre presentation, please send
abstract of research to cal@tc.cornell.edu by March 30, 1993.
========
WORKSHOP
========
In conjunction with the symposium, the Theory Center will conduct,
during May 5-7, a training workshop on using the KSR1 parallel
computer. A fee will be charged for the training workshop. Registration
available separately.
==============
ACCOMMODATIONS
==============
Two local hotels have set aside rooms for the nights of May 3-4. Please
make your reservations directly with the hotel and mention that you are
coming for the Simulation of Polypeptide and Protein Structure
symposium. Reservations must be made by April 12 to assure room
availability.
Sheraton Inn
One Sheraton Drive
Ithaca, NY 14850
607-257-2000 or 1-800-257-6992
607-257-3998 (fax)
Rates start at $62
Holiday Inn
2310 North Triphammer Road
Ithaca, NY 14850
607-257-3100 or 1-800-465-4329
607-257-4425 (fax)
Rates start at $60
=================
REGISTRATION FORM
=================
Return this part only, by April 5:
Symposium on Simulation of Polypeptide
and Protein Structure
May 3-4, 1993
Sheraton Inn and Conference Center, Ithaca, NY
Name: __
Title: __
Organization: __
Address: __
City/State/Zip/Country: __
Phone/Fax: __
Email: __
Special dietary requirements:
Kosher__
Vegetarian__
Other ________________________________________
Return completed form to:
(deadline April 5, 1993)
Donna Smith, Conference Coordinator
422 Theory Center
Cornell University
Ithaca, NY 14853
607-254-8686; 607-254-8888 (fax)
donna@tc.cornell.edu
--end post--
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Ph.d Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From F0388913@JAGUAR.CSC.WSU.EDU Thu Apr 1 15:43:20 1993
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id AA15220; Thu, 1 Apr 93 15:43:20 -0500
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(for charmm-bbs@emperor) id AA06865; Thu, 1 Apr 93 15:40:15 EST
Date: Thu, 1 Apr 1993 12:40:10 -0800 (PST)
From: F0388913@JAGUAR.CSC.WSU.EDU (Brian W. Beck)
Message-Id: <930401124010.2060c02a@JAGUAR.CSC.WSU.EDU>
Subject: Equilibration Suggestions?
To: charmm-bbs%emperor@harvard
X-Vmsmail-To: SMTP%"charmm-bbs%emperor@harvard.harvard.edu"
As I've written before, I've been trying to make a box
of dimethyl formamide as a solvent, and now I've got it
going, but I wanted a test for equilibration because I've
started from a simple cubic lattice and I'm trying
to get to a liquid.
Refering to Allen & Tildesley, I've tried using the the
translational order parameter:
N
1 __
rho(k)= - \ cos(k*ri)
N /_
i
where k is the a reciprocal lattice vector of the initial lattice
and ri is the position vector of atom i.
To keep rho(k) origin-independent, I've actually calculated the
the sqrt of the sum of the square of the above function plus the
square of a similar sine function.
However, what I observe happening is the simulation starts partially
disorderd (remember I started from a randomly oriented cubic lattice)
and generally remains so across my simulation.
1st:
What methods do the rest of you use to test equilibration of
novell liquid systems?
2nd:
Has anyone used the translational order parameter before
and run into similar phenomena?
Any suggestions would be greatly appreciated.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
From scsupham@reading.ac.uk Fri Apr 2 04:47:23 1993
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From: scsupham@reading.ac.uk
Date: Fri, 2 Apr 93 10:35:31 BST
Message-Id: <2210.9304020935@scsscsc3>
To: charmm-bbs <@harvard:charmm-bbs@emperor>
Subject: Scaling of 1,4 ES interactions
Cc: scsupham@reading.ac.uk, jasmit@chemistry.reading.ac.uk
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1,4 electrostatic interactions are scaled by 0.5 in CHARMm, but I have been unable to find any justification for this. Would it be invalid to alter the scaling factor to 1.0 when using ESP derived charges? Is the scaling factor required to reproduce correct torsional barriers and exists as a result of the setup of torsional and non-bonded parameterisation.
jasmit.
John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK.
Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet)
Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610
----------
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X-Sun-Content-Lines: 3
John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK.
Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet)
Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610
END --> chmbbs-mar93.log <---
BEGIN --> chmbbs-apr93.log <---
From F0388913@JAGUAR.CSC.WSU.EDU Thu Apr 1 15:43:20 1993
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(for charmm-bbs@emperor) id AA06865; Thu, 1 Apr 93 15:40:15 EST
Date: Thu, 1 Apr 1993 12:40:10 -0800 (PST)
From: F0388913@JAGUAR.CSC.WSU.EDU (Brian W. Beck)
Message-Id: <930401124010.2060c02a@JAGUAR.CSC.WSU.EDU>
Subject: Equilibration Suggestions?
To: charmm-bbs%emperor@harvard
X-Vmsmail-To: SMTP%"charmm-bbs%emperor@harvard.harvard.edu"
As I've written before, I've been trying to make a box
of dimethyl formamide as a solvent, and now I've got it
going, but I wanted a test for equilibration because I've
started from a simple cubic lattice and I'm trying
to get to a liquid.
Refering to Allen & Tildesley, I've tried using the the
translational order parameter:
N
1 __
rho(k)= - \ cos(k*ri)
N /_
i
where k is the a reciprocal lattice vector of the initial lattice
and ri is the position vector of atom i.
To keep rho(k) origin-independent, I've actually calculated the
the sqrt of the sum of the square of the above function plus the
square of a similar sine function.
However, what I observe happening is the simulation starts partially
disorderd (remember I started from a randomly oriented cubic lattice)
and generally remains so across my simulation.
1st:
What methods do the rest of you use to test equilibration of
novell liquid systems?
2nd:
Has anyone used the translational order parameter before
and run into similar phenomena?
Any suggestions would be greatly appreciated.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
From scsupham@reading.ac.uk Fri Apr 2 04:47:23 1993
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id <28078-0@susssys1.reading.ac.uk>; Fri, 2 Apr 1993 10:35:19 +0100
From: scsupham@reading.ac.uk
Date: Fri, 2 Apr 93 10:35:31 BST
Message-Id: <2210.9304020935@scsscsc3>
To: charmm-bbs <@harvard:charmm-bbs@emperor>
Subject: Scaling of 1,4 ES interactions
Cc: scsupham@reading.ac.uk, jasmit@chemistry.reading.ac.uk
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1,4 electrostatic interactions are scaled by 0.5 in CHARMm, but I have been unable to find any justification for this. Would it be invalid to alter the scaling factor to 1.0 when using ESP derived charges? Is the scaling factor required to reproduce correct torsional barriers and exists as a result of the setup of torsional and non-bonded parameterisation.
jasmit.
John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK.
Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet)
Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610
----------
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John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK.
Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet)
Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610
From brian@opus.chem.psu.edu Fri Apr 2 10:36:16 1993
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Date: Fri, 2 Apr 1993 10:33:57 -0500
From: brian@opus.chem.psu.edu (Brian J. Toleno)
Message-Id: <9304021533.AA21180@opus.chem.psu.edu>
To: charmm-bbs%emperor@harvard
I was wondering if anyone out there had a way to make RTFs from Gaussian92
or MOPAC files, or anyway to get geometries, etc. results from these progs
into Quanta 3.2 (yes, its the old one). Thanks in advance.
BT
brian@opus.chem.psu.edu
From kuczera@tedybr.chem.ukans.edu Fri Apr 2 13:41:09 1993
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Date: Fri, 2 Apr 1993 12:36:01 -0600
From: kuczera@tedybr.chem.ukans.edu
Message-Id: <9304021836.AA14982@tedybr.chem.ukans.edu>
To: charmm-bbs
In response to John Upham on the 1,4 factor:
E14F = 0.5 (and sometimes even = 0.4) was used in previous
CHARMM parametrizations to scale down 1-4 electrostatic (and van der
Waals) interactions. As you mention, the reasons for this are not
clear today; certainly it is only a slight complication and does no
harm. All sorts of parameter values specifying equilibrium
geometries and force constants are in principle dependent on the
value of E14F.
In the CHARMM version 22 parameter set we decided to simplify things
and use E14F = 1.0. Surprisingly, modifying this parameter from
0.5 to 1.0 does not change things a lot, even for charged systems
like the acetate ion (things = vibrational spectra, torsional barriers).
For the model molecules I worked on, I found that generally only slight
modifications of the dihedral force constants were needed, if any.
To summarize, as you might expect, if you are parametrizing new
molecules it makes sense to use E14F = 1.0 as long as you check that
this does not introduce problems when merging new and old parameters.
Krzysztof Kuczera
Department of Chemistry
University of Kansas
2010 Malott Hall
Lawrence, KS 66045
tel: (913) 864-5060 (my office) or 864-4670 (Chemistry office)
fax: (913) 864-5396
e-mail: kuczera@tedybr.chem.ukans.edu
chant: rock-chalk-jayhawk
From brbrooks@helix.nih.gov Fri Apr 2 14:58:48 1993
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Date: Fri, 2 Apr 93 14:55:43 -0500
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9304021955.AA19175@helix.nih.gov>
To: charmm-bbs%emperor@harvard, kuczera@tedybr.chem.ukans.edu
Subject: More on 1-4 electrostatics.
In response to John Upham and Krzysztof Kuczera regarding 1-4 electrostatics.
During the development of PARAM19 in 1984, we ran a number of crystal
simulations (mostly cyclohexapeptides with 1-3 waters). We examined
a wide variety od 1-4 factors and found that a factor of 0.4 gave optimal
agreement with the crystal structures. Wheras it is true that a suboptimal
1-4 scale factor can be compensated for with adjusting torsional parameters,
we have found this to be difficult to do in a general manner for transferable
potential terms (i.e. quick fixes are generally not transferable).
We have found that a 0.4-0.5 electrostatic scale factors are a good bridge
betweed 1-3 interactions (not computed) and 1-5 interactions (fully calculated).
This reduces the problems associated with splitting dipoles. For example,
the C5 conformation of the alainine dipeptide is destabilized with a full
1-4 interaction (two repusive and one attractive interactions). With a
0.5 scale factor, there are two half repulsive and one attractive interaction.
My recommendation is to use a scale factor of 0.5 for future parameter
deveopment work. It is easier and the parameters are more transferable.
Bernie Brooks, NIH'
From brian@opus.chem.psu.edu Mon Apr 5 13:56:44 1993
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Date: Mon, 5 Apr 1993 13:55:12 -0400
From: brian@opus.chem.psu.edu (Brian J. Toleno)
Message-Id: <9304051755.AA13596@opus.chem.psu.edu>
To: charmm-bbs%emperor@harvard
I was wondering if anyone out there had a way to make RTFs from Gaussian92
or MOPAC files, or anyway to get geometries, etc. results from these progs
into Quanta 3.2 (yes, its the old one). Thanks in advance.
BT
brian@opus.chem.psu.edu
From milan@helix.nih.gov Mon Apr 5 17:32:31 1993
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Date: Mon, 5 Apr 93 17:28:26 -0400
From: milan@helix.nih.gov (Milan Hodoscek)
Message-Id: <9304052128.AA08837@helix.nih.gov>
To: brian@opus.chem.psu.edu (Brian J. Toleno)
Cc: charmm-bbs%emperor@harvard
In-Reply-To: <9304051755.AA13596@opus.chem.psu.edu>
References: <9304051755.AA13596@opus.chem.psu.edu>
Brian J. Toleno writes:
>
>
>
> I was wondering if anyone out there had a way to make RTFs from Gaussian92
> or MOPAC files, or anyway to get geometries, etc. results from these progs
> into Quanta 3.2 (yes, its the old one). Thanks in advance.
>
> BT
> brian@opus.chem.psu.edu
>
>
Hi,
I made a program which makes charmm input file to see movies out of
gaussian output with charmm graphics on Apollo or with quanta...
Regards -- Milan Hodoscek
From chandra@yorvic.york.ac.uk Tue Apr 6 13:55:34 1993
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From: Chandra Verma <chandra@yorvic.york.ac.uk>
Date: Tue, 6 Apr 93 18:52:18 GMT
Message-Id: <10936.9304061852@bill>
To: charmm-bbs%emperor@edu.harvard.harvard
Subject:
Has anyone examined the effect of mixing all-atom and extended potentials in a
simulation. For example what happens if say a protein is represented by an
extended atom potential and a ligand that binds to the protein by an all atom
potential. If so, what happens?
From hong@dna.chm.jhu.edu Tue Apr 6 17:56:34 1993
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Date: Tue, 6 Apr 93 17:48:47 -0400
From: hong@dna.chm.jhu.edu (Guo Hong)
Sender: hong@dna.chm.jhu.edu
To: charmm-bbs
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Apparently-To: charmm-bbs
subscribe charmm-bbs
From mitchell_t%frgen.dnet@smithkline.com Wed Apr 7 04:40:11 1993
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Date: Wed, 7 Apr 93 04:05:34 -0400
Message-Id: <9304070805.AA18699@smithkline.com>
From: mitchell_t%frgen.dnet@smithkline.com
To: charmm_bbs@smithkline.com.local
Subject: Mixing all atom and extended potentials
If the ligand is a non-peptide, then it would seem sensible to use
extended potentials for the protein (to reduce the non-bonded list)
and all atom-potentials for the ligand -- I presume I'm right in
thinking that the parameter development for small molecules is done with
all atom-potentials.
I have mixed the two and got "sensible" results.
Original query follows.........
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax. (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || mitchell_t%frgen.dnet@smithkline.com U.K. |
-------------------------------------------------------------------------------
From: INET::"chandra@yorvic.york.ac.uk" 6-APR-1993 18:58:32.21
To: charmm-bbs%emperor@edu.harvard.harvard
CC:
Subj:
Has anyone examined the effect of mixing all-atom and extended potentials in a
simulation. For example what happens if say a protein is represented by an
extended atom potential and a ligand that binds to the protein by an all atom
potential. If so, what happens?
From Cathy_Terwedow@MSI.COM Wed Apr 7 16:01:04 1993
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Message-Id: <9304071954.AA10882@schizoid.msi.com>
Date: 7 Apr 1993 15:54:28 +0000
From: "Cathy Terwedow" <Cathy_Terwedow@MSI.COM>
Subject: Force Field Development Sem
To: "All CHARMm Users" <Charmm-Bbs>
Cc: Frank_Momany@MSI.COM
Subject: Time:2:49 PM
OFFICE MEMO Force Field Development Seminar Date:4/7/93
Scientific Seminar
FORCE FIELD DEVELOPMENT
Monday, April 26
16 New England Executive Park
Burlington, MA
Molecular Simulations Incorporated invites you to visit their corporate
headquarters for a one-day seminar on force-field parameter development,
refinement methods, and recent results of calculations.
10:00 Frank Momany, Molecular Simulations Inc.
Introduction
10:15 Lothar Schafer, The University of Arkansas
Recent Results from Geometry Refined Correlation ab initio Studies and
their Use in the Development of Empirical Force Field Parameters
11:15 Bernard Brooks, The National Institutes of Health
Evaluation of Macromolecular Force Field Parameters through Molecular
#011#Dynamic Simulations
12:15 Lunch, Discussion
1:30 Kjeld Rassmussen, The Technical University of Denmark
The Consistent Force Field: Development of Potential Energy Functions by
Optimization of Experimental Data
2:30 Thomas Halgren, Merck Research Laboratories
The MMFF Force Field: Development of Potential Energy Parameters and
#011#functions using ab initio Results
3:30 Break
3:45 Frank Momany, MSI
Use of QUANTA(r) 3.3/CHARMm(r) Parameters on Small to Medium Size Cyclic and
Linear Peptides
4:40 Discussion and Conclusion
Reservations are requested. Please fax your response to Cathy Terwedow,
617/229-9899. If you prefer, you can call our seminar information line at
617/229-9800 x567 and make your reservation by voice mail.
From Cathy_Terwedow@MSI.COM Wed Apr 7 16:28:41 1993
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Date: 7 Apr 1993 16:23:33 +0000
From: "Cathy Terwedow" <Cathy_Terwedow@MSI.COM>
Subject: Momany Seminar
To: "All CHARMm Users" <Charmm-Bbs>
Cc: Frank_Momany@MSI.COM
Subject: Time:3:21 PM
OFFICE MEMO Momany Seminar Date:4/7/93
I just sent out a notice to the CHARMm bulletin board about a seminar on force
field development being held at Molecular Simulations' headquarters in
Burlington, MA. If you wish to register for this seminar, PLEASE give me your
name, address, phone and fax numbers, as well as your academic or corporate
affiliation and title! Just saying "Yes, I'll attend" is not enough!
Thank-you,
Cathy Terwedow
Manager of Marketing Communications
Molecular Simulations
From W.P.vanHoorn@ct.utwente.nl Thu Apr 15 08:11:42 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9304151305.AA27304@utctu6.ct.utwente.nl>
Subject: Hydrogen-bond display parameters Quanta
To: charmm-bbs (CHARMm BBS)
Date: Thu, 15 Apr 1993 14:04:59 +0000 (WDT)
X-Mailer: ELM [version 2.4 PL5]
Content-Type: text
Content-Length: 1244
Hi,
When I let Quanta draw hydrogen bonds it seems that it doesn't recognize
certain N-types as hydrogen-bond acceptors.
The parameters for deciding whether an atom is a donor or an acceptor
are found in $HYD_LIB/param.par (Is this true??). In this file only
the following N-types are marked as acceptors:
N5R Nitrogen in a five membered aromatic ring
N6R Nitrogen in a six membered aromatic ring
N6RP for Aryl-Aryl bond between six membered rings
At least I should have expected the following N-type also marked as
acceptors:
NT Nitrogen (tetrahedral), i.e. Amine, etc.
NP Nitrogen in peptide, amide, or related, group
NC Charged guanidinium-type nitrogen
NC2 for neutral guanidinium group - Arg sidechain
...
Does anyone know why these parameters are set up as they are?
Thanks,
----------------------------------------------------------------------
Willem Paul van Hoorn (ir.)
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (NL)53-892955
P.O. Box 217 (NL)53-892980
7500 AE Enschede, The Netherlands fax : (NL)53-356024
----------------------------------------------------------------------
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Fri Apr 16 17:39:13 1993
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Date: Fri, 16 Apr 93 17:06:17 EDT
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: Reply to van Horn
To: CHARMM-BBS
The other atoms you mentioned usually have a polar hydrogen attached
which serves as a hydrogen bond donor, No?
From MEMMS@CUNYVM.CUNY.EDU Tue Apr 20 12:06:35 1993
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Date: Tue, 20 Apr 93 12:00:03 EDT
From: Mihaly Mezei <MEMMS@cunyvm>
Subject: Inclusion
To: Charmm BB <charmm-bbs%emperor@harvard>
Greetings,
Could you please add me to the Charmm mailing list? Thank you.
Mihaly Mezei
MEMMS@CUNYVM.CUNY.EDU
Dept. of Physiology and Biophysics
Mount Sinai School of Medicine
New York, NY 10029
From W.P.vanHoorn@ct.utwente.nl Thu Apr 22 04:12:46 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9304220906.AA28032@utctu6.ct.utwente.nl>
Subject: Answers Hydrogen display Quanta
To: charmm-bbs (CHARMm BBS)
Date: Thu, 22 Apr 1993 10:06:13 +0000 (WDT)
X-Mailer: ELM [version 2.4 PL5]
Content-Type: text
Content-Length: 2478
I have sent the following question to the CHARMm BBS:
>When I let Quanta draw hydrogen bonds it seems that it doesn't recognize
>certain N-types as hydrogen-bond acceptors.
>The parameters for deciding whether an atom is a donor or an acceptor
>are found in $HYD_LIB/param.par (Is this true??). In this file only
>the following N-types are marked as acceptors:
>N5R Nitrogen in a five membered aromatic ring
>N6R Nitrogen in a six membered aromatic ring
>N6RP for Aryl-Aryl bond between six membered rings
>At least I should have expected the following N-type also marked as
>acceptors:
>NT Nitrogen (tetrahedral), i.e. Amine, etc.
>NP Nitrogen in peptide, amide, or related, group
>NC Charged guanidinium-type nitrogen
>NC2 for neutral guanidinium group - Arg sidechain
>...
>Does anyone know why these parameters are set up as they are?
Chandra Verma <chandra@yorvic.york.ac.uk> answers:
>If you look at $HYD_LIB there is a file called dictionary.lib. Copy that file
>into the area you are running quanta from or maybe in your home area (you will
>have to test this out). then copy the param.par file into some area and put in
>the missing atom types or change any atom types to what you want. then edit
>dictionary.lib and include a line which points to your file and when you look
>at the EDIT menu there is apply dictionary option - use it and the files in
>dictionary.lib ought to come up including your file and use it. why the status
>is as at present i haven't a clue!
MSI Technical Support Hotline <hotline@msi.com> answers:
> The nitrogen types you specify are more typically regarded as donors for
>hydrogen bonds rather than acceptors. In the Quanta method, though, the
>hydrogen itself is marked as the donor (rather than the heavy atom, as is done
>in CHARMm).
>
> If you want these nitrogens to be involved in hydrogen bonding in an
>acceptor role, you can make the changes in $HYD_LIB/param.par to convert them
>to acceptors.
>
> Bob Funchess
Thanks for all answers,
Regards,
----------------------------------------------------------------------
Willem Paul van Hoorn (ir.)
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (NL)53-892955
P.O. Box 217 (NL)53-892980
7500 AE Enschede, The Netherlands fax : (NL)53-356024
----------------------------------------------------------------------
From chandra@yorvic.york.ac.uk Fri Apr 23 05:24:20 1993
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From: Chandra Verma <chandra@yorvic.york.ac.uk>
Date: Fri, 23 Apr 93 10:20:36 GMT
Message-Id: <4314.9304231020@dibble>
To: charmm-bbs%emperor@edu.harvard.harvard
Subject:
Venable et al have just published a report on the dynamics of HIV-1 Protease
in a sperical aqueous droplet in Proteins (vol 15). The waters are prevented
from flying off by applying a weak centripetal force which approximates an
external pressure of 2 atmospheres. has anyone any idea of how these dynamics
compare with those with the waters restrained from flying off by fixing only
the outer layer or two of the sphere and leaving the rest of the waters free
chandra
From chin@thurifer Tue Apr 27 16:07:00 1993
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Date: Tue, 27 Apr 93 16:07:47 EDT
From: chin@thurifer (Donovan Chin)
To: charmm-bbs
Subject: New charmm-bbs version..
Greetings,
Due to the size and complexity of the existing charmm-bbs (> 150 members
with 10 addresses to other groups), I have put together a new version
of the charmm-bbs exploder program (many thanks Jan).
The existing charmm-bbs can be fooled every now-and-then by faulty e-mail
addresses and/or downed systems, much to the inconvenience of many of it's
subscribers.
The new charmm-bbs will be more "intelligent" and "administrative" so that
an acceptable level of reliability will be consistently maintained.
Before I fully implement the new charmm-bbs, I would like to solicit a
few volunteers from the charmm-bbs community to test the new system.
Ideally, I would like to have a wide sample of e-mail addresses if possible.
If you think you have an unusual e-mail address or mail program, I would
appreciate it if you consider taking time out to be a volunteer. The tests
will be very short...more on this if you are willing.
If you are able to be a tester, then send e-mail stating so to:
chin@thurifer.harvard.edu.
I will respond at the appropriate time when I have gathered enough people.
Regards, Donovan
charmm-bbs-administrator.
From chind@cobalt.ulowell.edu Tue Apr 27 17:06:08 1993
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From: chind@cobalt.ulowell.edu
Message-Id: <9304272100.AA13388@cobalt.ulowell.edu>
To: charmm-bbs
Subject: What is PSTRCT in charmm?
** I am posting this for jarrinm@woods.ulowell.edu **
---------------------------------------------------------------------------
U N I V E R S I T Y O F M A S S A C H U S E T T S L O W E L L
Subject: Meaning of PSTRCT?
I am trying to do an energy minimization using the algorithm ABNR
(Adopted basis Newton-Raphson). The number of steps for the minimization is
10000 (NSTEP=10000) and the tolerance applied to the average gradient
is set to 0.10 (TOLGRD=0.10). Before the minimization starts, the following
message is sent to the LOG file:
"ABNER> An energy minimization has been requested"
This is followed by a list of 12 keywords, such as TOLGRD and NSTEP, and their
respective numerical values. Among these keywords there is one named
PSTRCT=0.0001 Soon after this message minimization starts, but it sops
before the total number of steps or before arriving to a TOLGRD=0.10.
Instead the message sent to the LOG file is:
"ABNER> Minimization exiting with variable tolerance (0.0001) satisfied"
I believe that the message is reffering to PSTRCT since is the only keyword
set to a value of 0.0001 Can somebody tell me what PSTRCT stands for?
I searched $CHM_DATA/doc but I could not find information about PSTRCT.
I am using CHARMm 21.3
I would really appreciate any information about this problem, thank you.
Mario Jarrin
Chemistry Department
U. of Massachusetts at Lowell
One University Ave.
Lowell, MA 01854
508-934-3708/3541
e-mail: jarrinm@woods.ulowell.edu
From ryszard@MSI.COM Tue Apr 27 17:40:25 1993
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Date: Tue, 27 Apr 1993 17:36:45 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9304272136.AA04324@hogan.MSI.COM>
To: charmm-bbs%emperor@harvard, chind@cobalt.ulowell.edu
Subject: Re: What is PSTRCT in charmm?
If coordinates are moving less then PSTRCT abner stops with the message
"ABNER> Minimization exiting with variable tolerance <PSTRCT> satisfied".
Actually it is testing biggest RELATIVE displacement
maximum (abs(par_new(i) - par_old(i))/par_old(i))
In charmm22 default value for PSTRCT is set to zero.
Ryszard, MSI
From chin@thurifer Wed Apr 28 20:42:39 1993
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Date: Wed, 28 Apr 93 20:43:27 EDT
From: chin@thurifer (Donovan Chin)
To: charmm-bbs
Subject: I have enough testers...
..for the new charmm-bbs.
Thanks,
Donovan Chin
charmm-bbs-administrator.
From UCH422@unidozr.hrz.uni-dortmund.de Thu Apr 29 06:52:39 1993
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Date: Thu, 29 Apr 93 12:48:55 SET
From: wos <UCH422@unidozr.hrz.uni-dortmund.de>
Subject: correl
To: charmm-bbs@emperor.harvard.edu.
****************************************************************
I HOPE THIS MESSAGE IS NOW CORRECTLY ADDRESSED!!!!!
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
DEAR MRS. AND MR.,
I HAVE SOME PROBLEMS IN CALCULATING CORRELATION FUNCTIONS AND
FLUCTATIONS WITH QUANTA/CHARMM3.3
I HAVE SIMULATED A SYSTEM OF 50 MOLECULES OF A LIQUID CRYSTAL,
4-(T-4'-N-PENTYL-CYCLOHEXYL)-BENZONITRIL, WITH PERIODIC BOUNDARY
CONDITIONS.
I WANT TO GENERATE A STREAM FILE TO CALCULATE CORRELATION FUNCTIONS,
MEAN SQUARE DISPLACEMENT OF CENTRE OF MASS ETC. THEREFORE I WANT TO
USE THE KEYWARDS CORFUN AND CORREL. THE ENTER KEYWORD IS NECESSARY
TO SPECIFY THE ATOMS, BONDS AND DIHEDRALS TO CHECK WHICH FUNCTIONS
ARE TO BE CALCULATED.
MY PROBLEM IS TO DEFINE THESE DECLARATIONS. I CAN USE ATOM TYPES OR
ATOM NUMBERS BUT THE CALCULATION INTERRUPTS WITH
ERROR 'UNREGOGNIZED ATOMS/COMMANDS'.
PLEASE TELL HOW I CAN GENERATE THE CORRECT STREAM FILE FOR THE PROBLEMS
I HAVE DESCRIBED ABOVE. WHICH KEYWORD CALCULATES THE CENTRE OF MASS?
THE MEANING OF THE KEYWORDS MAXTIME AND MAXSERIES ARE NOT CLEAR DEFINED
WITH REGARD TO THE KEYWORD CORFUN.
BEST REGARDS,
B. WOSNIK
From UCH422@unidozr.hrz.uni-dortmund.de Thu Apr 29 08:24:40 1993
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Thu, 29 Apr 93 14:21:22 SET
Date: Thu, 29 Apr 93 14:20:58 SET
From: wos <UCH422@unidozr.hrz.uni-dortmund.de>
Subject: shape
To: charmm-bbs@emperor.harvard.edu.
DEAR MRS. AND MR.,
I HAVE SIMULATED A SYSTEM OF 50 MOLECULES OF A LIQUID CRYSTAL AND DONE
A CONSTANT PRESSURE AND TEMPERATURE CALCULATION WITH PERIODIC BOUNDARIES
(CUBIC SYSTEM)
FURTHERMORE I WANT TO USE MY *.DCD FILES FOR EXTERNAL CALCULATIONS.
THEREFORE I TRY TO CONVERT THESE .DCD FILES INTO IOBUFFER-FORMAT, BUT
I DON'T KNOW THE ADDITIONAL INFORMATIONS ABOUT THE SYMMETRIC SHAPE
MATRIX XTLABC WHEN QCRYS=TRUE. ==> USERS'S GUIDE SUPPLEMENT S.156!!!!
PLEASE TELL ME ABOUT THE WAY TO DEFINE THIS EXPRESSION AS SOON AS
POSSIBLE.
THANKS,
BEATE WOSNIK
From ryszard@MSI.COM Thu Apr 29 11:45:23 1993
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Date: Thu, 29 Apr 1993 11:41:34 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9304291541.AA15644@hogan.MSI.COM>
To: UCH422@unidozr.hrz.uni-dortmund.de, charmm-bbs%emperor@harvard
Subject: Re: shape
Dear Beate,
Symmetric shape matrix XTLABC is stored in DCD file as a low triagle.
It means in general:
S11
S12 S22
S13 S23 S33
In your case:
A
0 B
0 0 C
(since you are dealing with CUBIC system).
If you have any further problems with it, let me know and we can deal
with it off line.
Sincerely,
Ryszard Czerminski, MSI
From dchin Thu Apr 29 14:54:50 1993
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Date: Thu, 29 Apr 93 14:54:50 -0400
From: dchin (Donovan Chin)
Message-Id: <9304291854.AA05048@emperor.harvard.edu>
To: mytest
Subject: test
This is a test
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From dchin Thu Apr 29 14:55:46 1993
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Date: Thu, 29 Apr 93 14:55:46 -0400
From: dchin (Donovan Chin)
Message-Id: <9304291855.AA05064@emperor.harvard.edu>
To: mytest
Subject: Test
This is just a test
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From dchin Thu Apr 29 14:59:35 1993
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From: dchin (Donovan Chin)
Message-Id: <9304291859.AA05105@emperor.harvard.edu>
To: bbs-log
Subject: dkfj
dkfjk
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From dchin Thu Apr 29 15:00:46 1993
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Date: Thu, 29 Apr 93 15:00:46 -0400
From: dchin (Donovan Chin)
Message-Id: <9304291900.AA05133@emperor.harvard.edu>
To: bbs-log
Subject: dkfj
kdjf
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From dchin Thu Apr 29 15:01:25 1993
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Date: Thu, 29 Apr 93 15:01:25 -0400
From: dchin (Donovan Chin)
Message-Id: <9304291901.AA05145@emperor.harvard.edu>
To: mytest
Subject: dkfjk
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From chind@cobalt.ulowell.edu Thu Apr 29 15:02:24 1993
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Date: Thu, 29 Apr 1993 14:57:00 -0400
From: chind@cobalt.ulowell.edu
Message-Id: <9304291857.AA10985@cobalt.ulowell.edu>
To: mytest
Subject: test cobalt
~r test.let
Citizens:
This is short message which serves only to test on
the charmm-bbs. It has more than 100 characters so
that charmm-bbs will not think it is a subscription.
This mindless dribble is from a temporary state of mind
and not indicative of the state I live in.
Vivaldi
From chind@cobalt.ulowell.edu Thu Apr 29 15:04:57 1993
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Date: Thu, 29 Apr 1993 14:59:32 -0400
From: chind@cobalt.ulowell.edu
Message-Id: <9304291859.AA05118@cobalt.ulowell.edu>
To: mytest
Subject: test
Citizens:
This is short message which serves only to test on
the charmm-bbs. It has more than 100 characters so
that charmm-bbs will not think it is a subscription.
This mindless dribble is from a temporary state of mind
and not indicative of the state I live in.
Vivaldi
'
From dchin Thu Apr 29 15:07:39 1993
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Date: Thu, 29 Apr 93 15:07:39 -0400
From: dchin (Donovan Chin)
Message-Id: <9304291907.AA05189@emperor.harvard.edu>
To: mytest
Subject: theh
dfjdk
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From dchin Thu Apr 29 15:27:10 1993
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Date: Thu, 29 Apr 93 15:27:10 -0400
From: dchin (Donovan Chin)
Message-Id: <9304291927.AA05228@emperor.harvard.edu>
To: mytest
Subject: charmm-bbs2.0 **Start over **
Dear testers,
Some of you did not get the message below because I had decided to use a
SUN for the bbs. Well as I found out, SUN does funny convoluted things with
certain email addresses. Consequently some of you didnt get the original
messaged. I am back to using a SGI now. THerefore "mytest@emperor.harvard.edu"
will be the address for the test.
This starting fresh. If are receiving this a second time, sorry, just reply back.
--Begin original message--
Greetings volunteers:
First, many thanks to all of you for taking part in the test
of the new charmm-bbs2.0.
"Ryszard Czerminski" "Robert Funchess"
"Boryeu Mao" "David Deerfield"
"Brian Beck" "Djamal Bouzida"
"Eldbjoerg Heimstad" "Peter Grootenhuis"
"Marc Gingold" "Arne Elofsson"
"Thomas Hoeffel" "Angelo Rossi"
"Bruce Tidor"
** So that I know that this gets through, please reply **
Depending on your various time tables (as well as time
zones), the tests shouldn't take too long to complete.
Here are the highlights of the new charmm-bbs(2.0):
**
The address (after the tests) will still be
"charmm-bbs@emperor.harvard.edu".
**
Messages send to charmm-bbs are pre-processed to determine if
they are acceptable and then redirected to all the subscribers.
The main criteria for acceptability is as follows:
(1)Returned mail is trapped by charmm-bbs2.0 (e.g. if a
person's address is no longer valid or a machine is down
somewhere). It is sent to charmm-bbs-administrator.
(2)Charmm-bbs2.0 now requires that you use the Subject:
field. If you do not use the Subject field, it will send a
message back to you stating why you need to use the Subject
field along with your original message.
(3)If there are any key words such as "subscribe, sign, of,
please, add, remove, delete, drop" in the body of the message
AND the body of text is less than 100 characters; then it is
redirected to the charmm-bbs-administrator as it is probably
related to a subscription status.
(4)If the body of the text is less than 100 characters and
doesn't contain one of the keywords in (3), then it is sent
to charmm-bbs-administrator. This may be contain words not
acceptable for distribution to the list. NOTE: if the body
of text contains personal signatures as well, it is possible
that one line messages could go to the list.
(5)If the message is greater than 50 Kb it is rejected.
Once a message has been accepted by the charmm-bbs2.0 pre-
processor it will redirect to the list of subscribers.
**NEW** charmm-bbs2.0 will now send a confirmation letter to
the originator of each posted message stating that it was
RECEIVED and that it has been DISTRIBUTED (no more guessing).
The originator of a message will also receive a second copy
of the letter as it is distributed to the list . The look
and feel of charmm-bbs2.0 will be similar to the
computational chemistry bbs at ccl.net (so sue me).
When you see this message you will have an idea on what the
distributed charmm-bbs2.0 mail will look like.
As this message is getting long, I will send another message
describing the tests.
I'll be back at the appropriate time.
--Donovan
charmm-bbs-administrator.
~
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From ryszard@MSI.COM Thu Apr 29 15:35:44 1993
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Date: Thu, 29 Apr 1993 15:32:03 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9304291932.AA13861@hogan.MSI.COM>
To: dchin%emperor@harvard, mytest%emperor@harvard
Subject: Re: charmm-bbs2.0 **Start over **
Donovan,
I have got your test (only one).
The way you have described it will work -
looks good.
See you,
Ryszard
From arne@mango.mef.ki.se Fri Apr 30 03:27:05 1993
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From: arne@mango.mef.ki.se (Arne Elofsson)
Message-Id: <9304300923.AA15579@mango.mef.ki.se>
To: dchin%emperor@harvard (Donovan Chin)
Cc: mytest%emperor@harvard, arne@mango.mef.ki.se
Subject: Re: charmm-bbs2.0 **Start over **
In-Reply-To: (Your message of Thu, 29 Apr 93 15:27:10 D.)
<9304291927.AA05228@emperor.harvard.edu>
Date: Fri, 30 Apr 93 09:23:54 +0000
The second message also went true for
arne elofsson
From dchin Sat May 1 12:03:53 1993
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Date: Sat, 1 May 93 12:03:53 -0400
From: dchin (Donovan Chin)
Message-Id: <9305011603.AA07945@emperor.harvard.edu>
To: mytest
Subject: * Second round of tests...
Ok, so far so good. I have not heard from Peter, Marc (the link to france
was down last week) or Angelo but they can catch up later.
Now I would like to test two things.
Tests:
(1) Will each of you send a message to mytest@emperor.harvard.edu that
is longer than 100 characters (including signatures), BUT DONT
INCLUDE A SUBJECT.
Charmm-bbs2.0 should reject the letter and send it back to you with a
message stating why.
Put the line "test for NO SUBJECT field" in the body of text for
this test. If anyone gets this message delivered to them, please
let me know.
** When you get the rejected message back from charmm-bbs2.0,
please send a note to me at: "dchin@emperor.harvard.edu" **
next test
(2) Now send a message to mytest@emperor.harvard.edu that HAS a
subject field.
You may want to take this time to share any views you may have
about this bbs. I welcome any suggestions.
Put the line " test DISTRIBUTED message" in the body of the text.
** When everybody receives a message from everyone else, please send a note
to me at: "dchin@emperor.harvard.edu" **
Probably the best thing to do here is to collect the messages from
everyone for a day or so and then send me a message stating something
like, '..received messages from person1, person2, person3....etc.'
Thanks ahead of time,
--Donovan.
ps. once again; due to the different schedules of the testers,
messages may pop up slowly over time. This was written
Saturday April 4th.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From bobf@MSI.COM Sat May 1 12:33:37 1993
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id AA21428; Sat, 1 May 93 12:25:52 EDT
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for mytest@emperor.harvard.edu id AA06350; Sat, 1 May 93 12:29:34 -0400
Message-Id: <9305011629.AA06350@support>
From: Bob Funchess <bobf@MSI.COM>
Date: Sat, 1 May 1993 12:29:33 -0400
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: mytest
test for NO SUBJECT field
Now I have to come up with some sort of gunk to fill up the 100 character
limit. One line is 80 characters, so two lines should do it... even if spaces
don't count I should be there by now.
Bob F.
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From bobf@MSI.COM Sat May 1 12:36:58 1993
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for mytest@emperor.harvard.edu id AA06362; Sat, 1 May 93 12:32:51 -0400
Message-Id: <9305011632.AA06362@support>
From: Bob Funchess <bobf@MSI.COM>
Date: Sat, 1 May 1993 12:32:51 -0400
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: mytest
Subject: test two
test DISTRIBUTED message
written Saturday May 1 (Donovan, Saturday April 4th?? are you using the same
calendar as the rest of us?)
I just got new mail:
Mail Delivery Subs May 1 (68/2845) ** MESSAGE REJECTED
Presumably that's the first test.
I have a couple of questions about the new format, but maybe I should talk to
Donovan directly about those since I just saw him 5 minutes ago.
Bob F.
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From dchin Sat May 1 13:16:03 1993
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Date: Sat, 1 May 93 13:16:03 -0400
From: dchin (Donovan Chin)
Message-Id: <9305011716.AA08035@emperor.harvard.edu>
To: mytest
Subject: *Dates..
April 4th --> May 1st.
Dont ask.
--Donovan
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
From bobf@MSI.COM Sat May 1 14:12:14 1993
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Message-Id: <9305011808.AA06541@support>
From: Bob Funchess <bobf@MSI.COM>
Date: Sat, 1 May 1993 14:08:11 -0400
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: mytest
junk mail
has to be more than one hunder chars. adfjkalds f fdjkadslf dsjdfkl df
dsfjkl;ds f adsjkfl;ds fjdsafkl;sda fj f jkdsa;f df asdjfk;sad fsadjfk
asdfjaskdlf askd;lfjsakdf as fjasdkl;fjadsk fdjdsakf;ljasdlkfjewurjvcm
xkjxsenm
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From tidor@mycroft.wi.mit.edu Sat May 1 14:40:47 1993
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Message-Id: <9305011834.AA22572@mycroft.wi.mit.edu>
To: mytest
Date: Sat, 01 May 93 14:34:46 -0400
From: tidor@mycroft.wi.mit.edu
This is a test from tidor@mycroft.wi.mit.edu. There is no subject line
and the message has more than 100 characters. Will Charmm-bbs2.0 reject
this message? test for NO SUBJECT field
Bruce
From tidor@mycroft.wi.mit.edu Sat May 1 14:45:54 1993
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To: mytest
Subject: test2
Date: Sat, 01 May 93 14:39:53 -0400
From: tidor@mycroft.wi.mit.edu
test DISTRIBUTED message
This is a test message to mytest@emperor.harvard.edu from
tidor@mycroft.wi.mit.edu.
Cheers,
Bruce
From db3q@engcd.bu.edu Sat May 1 17:05:45 1993
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Date: Sat, 1 May 93 17:06:20 -0400
From: db3q@engcd.bu.edu (Djamal Bouzida)
Message-Id: <9305012106.AA17887@engcd.bu.edu.bu.edu>
To: mytest
test for NO SUBJECT field
>Tests:
>
>(1) Will each of you send a message to mytest@emperor.harvard.edu that
> is longer than 100 characters (including signatures), BUT DONT
> INCLUDE A SUBJECT.
>
> Charmm-bbs2.0 should reject the letter and send it back to you with a
> message stating why.
>
> Put the line "test for NO SUBJECT field" in the body of text for
> this test. If anyone gets this message delivered to them, please
> let me know.
>
> ** When you get the rejected message back from charmm-bbs2.0,
> please send a note to me at: "dchin@emperor.harvard.edu" **
>
--
Djamal Bouzida E-mail: db3q@engcd.bu.edu
From db3q@engcd.bu.edu Sat May 1 17:08:26 1993
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Date: Sat, 1 May 93 17:09:01 -0400
From: db3q@engcd.bu.edu (Djamal Bouzida)
Message-Id: <9305012109.AA17896@engcd.bu.edu.bu.edu>
To: mytest
Subject: subject goes here.
test DISTRIBUTED message
>next test
>
>(2) Now send a message to mytest@emperor.harvard.edu that HAS a
> subject field.
>
> You may want to take this time to share any views you may have
> about this bbs. I welcome any suggestions.
>
> Put the line " test DISTRIBUTED message" in the body of the text.
>
> ** When everybody receives a message from everyone else, please send a note
> to me at: "dchin@emperor.harvard.edu" **
>
> Probably the best thing to do here is to collect the messages from
> everyone for a day or so and then send me a message stating something
> like, '..received messages from person1, person2, person3....etc.'
--
Djamal Bouzida E-mail: db3q@engcd.bu.edu
From /PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@sprint.com Sun May 2 14:47:26 1993
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id AA09270; Sun, 2 May 93 14:47:26 -0400
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id AA18244; Sun, 2 May 93 14:44:01 -0400
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id 00ft1Ngua001; 2 May 93 18:43:29 UT
Date: 2 May 93 14:27:27-0400
From: /PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@sprint.com
To: "TELEMAIL-00000001 *"<MYTEST>
Subject: NOTE 05/02/93 14:39:00
Message-Id:
<"SSW 930502142726683041"*/PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@sprint.com>
To: OPENADDR--SSW
From: boryeu mao
Subject:
test for NO SUBJECT field
This message has more than 100 chars but no SUBJECT; it should be
returned by ch-bbs.
Since the address scheme for sending out the message from this site is
unusual, let's hope this will come through without the SUBJECT and thus get
rejected. Fingers crossed... Here it goes.....
------------------------------------------------------------------------
Boryeu Mao ph. 616-385-5550
facs. 616-385-7373
email
/PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@SPRINT.COM
------------------------------------------------------------------------
From /PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@sprint.com Sun May 2 15:23:27 1993
Received: from sprintf.merit.edu by emperor.harvard.edu via SMTP (920110.SGI/911001.SGI)
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id 00ft1vRua001; 2 May 93 19:19:22 UT
Date: 2 May 93 15:03:28-0400
From: /PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@sprint.com
To: "TELEMAIL-00000001 *"<MYTEST>
Subject: failed 'test for NO SUBJECTfield'
Message-Id:
<"SSW 930502150327683101"*/PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@sprint.com>
To: OPENADDR--SSW
From: boryeu mao
Subject: failed 'test for NO SUBJECTfield'
To: OPENADDR--SSW
2 May 1993
(A message to Donovan, but FYI for all who must have received my
'test for NO SUBJECT field' message.)
Donovan -
As I suspected, my test-1 (for NOT SUBJECT field) got distributed. Our
email protocol has a 'Subject' field that could not be deleted; thus I
tried test-1 with a subject field but no subject in it, which was considered
by your bbs setup to be a valid message to be posted.
Since my test-1 actually got distributed, it WAS my 'test DISTRIBUTED
message' to those participating in the new bbs testing then (as is this one).
------------------------------------------------------------------------
Boryeu Mao ph. 616-385-5550
facs. 616-385-7373
email
/PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/ADMD=TELEMAIL/C=US/@SPRINT.COM
------------------------------------------------------------------------
From F0388913@JAGUAR.CSC.WSU.EDU Sun May 2 23:35:32 1993
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id AA09435; Sun, 2 May 93 23:35:32 -0400
Date: Sun, 2 May 1993 20:32:02 -0700 (PDT)
From: "Brian W. Beck" <F0388913@JAGUAR.CSC.WSU.EDU>
To: mytest
Cc: F0388913@JAGUAR.CSC.WSU.EDU
Message-Id: <930502203202.21404399@JAGUAR.CSC.WSU.EDU>
------------------------------ CHARMM BBS -------------------------------
test for NO SUBJECT field
Well here goes. I'll assume that there won't be any
problems doing this, as I've had none before with other
subject line controlled list servers.
BTW, as of Sunday (May 2) at 8:30pm PDT
I've received 4 messages from testers.
bobf@msi.com
tidor@mycroft.wi.mit.edu
db3q@engcd.bu.edu
BORYEU.MAO@sprint.com.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
From F0388913@JAGUAR.CSC.WSU.EDU Sun May 2 23:41:50 1993
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Date: Sun, 2 May 1993 20:38:24 -0700 (PDT)
From: "Brian W. Beck" <F0388913@JAGUAR.CSC.WSU.EDU>
To: mytest
Cc: F0388913@JAGUAR.CSC.WSU.EDU
Message-Id: <930502203824.21404399@JAGUAR.CSC.WSU.EDU>
Subject: A subject for all seasons
------------------------------ CHARMM BBS -------------------------------
test DISTRIBUTED message
Well here goes. I'll assume that there won't be any
problems doing this, as I've had none before with other
subject line controlled list servers.
Donovan: my test #1 was rejected.
BTW, as of Sunday (May 2) at 8:30pm PDT
I've received 4 messages from testers.
bobf@msi.com
tidor@mycroft.wi.mit.edu
db3q@engcd.bu.edu
BORYEU.MAO@sprint.com.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
From eldbjorg@chem.uit.no Mon May 3 03:35:59 1993
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Date: Mon, 3 May 93 09:33:57 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9305030933.AA28775@trypsin.chem.uit.no>
To: mytest
test for NO SUBJECT field
This is monday morning in Tromsoe, North Norway. It is snowing outside, so it not much warm and not much looks like spring or summer.
This is a test with no subject and more than 100 words, I will
try to fill up
CHARMM> if 2 gt 1 join SOLV s@2 renumber
RDCMND substituted parameter 2 (2) : "80"
Comparing "80" and "1".
IF test evaluated as true. Performing command
***** LEVEL -1 WARNING FROM <JOINSG> *****
***** SECOND SEGMENT DOESNT FOLLOW FIRST
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 2
CHARMM> coor stat
STATISTICS FOR 3264 SELECTED ATOMS:
-----------------------------------------------------
Do you know if anyone else has experienced this, I got normal
termination and the system with protein together with
crystallographic water and TIP3 water looks OK in QUANTA.
The reason why I wanted to use CHARMm standalone is that QUANTA
does not like the residue numbering for trypsin as 188, 188A
188, 188A and 221, 221A. CHARMm handles this without changing any
residue numbers or renaming.
Say I want to do further calculations on my solvated sytem,
i) Should I minimise the bulk water first, before the whole system?
ii) How do I prevent my waters for
flying off by fixing only
the outer layer or two of the sphere and leaving the rest of the waters free?
--------
By the way, is it advicable to minimise the protein before solvating
in bulk water?
Do you know if anyone else has experienced this, I got normal
termination and the system with protein together with
crystallographic water and TIP3 water looks OK in QUANTA.
The reason why I wanted to use CHARMm standalone is that QUANTA
does not like the residue numbering for trypsin as 188, 188A
188, 188A and 221, 221A. CHARMm handles this without changing any
residue numbers or renaming.
Say I want to do further calculations on my solvated sytem,
i) Should I minimise the bulk water first, before the whole system?
ii) How do I prevent my waters for
flying off by fixing only
the outer layer or two of the sphere and leaving the rest of the waters free?
--------
By the way, is it advicable to minimise the protein before solvating
in bulk water?
Is there other important things to be aware of in calculations
(MM and MD) of a solvated sytem?
Thanks in advance,
Elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From arne@mango.mef.ki.se Mon May 3 03:44:06 1993
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Date: Mon, 3 May 93 09:40:59 GMT
From: arne@mango.mef.ki.se (Arne Elofsson)
Message-Id: <9305030940.AA18224@mango.mef.ki.se>
To: mytest
This is a test from Arne Elofsson.
"test for NO SUBJECT field"
Arne Elofson
bla bla bla bla bla bla bla
arne
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
From arne@mango.mef.ki.se Mon May 3 03:45:23 1993
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Date: Mon, 3 May 93 09:42:20 GMT
From: arne@mango.mef.ki.se (Arne Elofsson)
Message-Id: <9305030942.AA34617@mango.mef.ki.se>
To: mytest
Subject: Test with subjevt from Arne Elofsson
This is a test from Arne Elofsson.
" test DISTRIBUTED message"
Arne Elofson
bla bla bla bla bla bla bla
arne
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
bla bla bla bla bla bla bla
From eldbjorg@chem.uit.no Mon May 3 03:49:33 1993
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Date: Mon, 3 May 93 09:47:36 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9305030947.AA28822@trypsin.chem.uit.no>
To: mytest
Subject: test2
test DISTRIBUTED message
My first mail (test 1) was rejected from MAILER-DAEMON.....
I have received 5 messages until now:
Dr. Robert B. Funchess
Bruce tidor@mycroft.wi.mit.ed
Djamal Bouzid
Boryeu Mao (as you know test1 also)
Brian W. Beck
It seems to work fine!
-elle By the way, it is snowing outside!
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From rossi@watson.ibm.com Mon May 3 07:49:11 1993
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Message-Id: <9305031145.AA50887@sandcastle.watson.ibm.com>
To: mytest
Subject: Test1
Date: Mon, 03 May 93 07:45:44 -0500
From: "Angelo R. Rossi (914-945-2834)" <rossi@watson.ibm.com>
Donavan:
I apologize for the the delay in testing, but, as the French say
"mieux vaux tard que jamais". I put this in here so that the
European counterparts would think we are suave and chic.
Angelo
From rossi@watson.ibm.com Mon May 3 07:53:25 1993
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To: mytest
Date: Mon, 03 May 93 07:49:59 -0500
From: "Angelo R. Rossi (914-945-2834)" <rossi@watson.ibm.com>
This is test 2. This is test #2. Or is it Test number 2. If not
then it must be test number two. That is all.
Angelo
From UCH422@unidozr.hrz.uni-dortmund.de Mon May 3 08:47:39 1993
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Mon, 03 May 93 14:44:07 SET
Date: Mon, 03 May 93 14:43:36 SET
From: wos <UCH422@unidozr.hrz.uni-dortmund.de>
Subject: s2
To: charmm-bbs@emperor.harvard.edu.
DEAR RYSZARD,
PLEASE TELL ME THE WAY I HAVE TO ADD THE EXTRA INFORMATION ABOUT THE
SHAPE MATRIX. I DON'T KNOW EXACTLY HOW I MUST DESCRIBE THIS ADDITION.
IN FORTRAN CODE.
FURTHERMORE I WANT TO USE THE KEYWORDS CORREL AND CORFUN TO CALCULATE
CORRELATION FUNCTIONS AND MEAN SQUARE DISPLACEMENT OF CENTRE OF MASS
BUT I HAVE SOME PROBLEMS IN GENERATING THE STREAM FILE FOR INSTANTS
TO DEFINE THE KEYWORD ENTER IF THE SYSTEM CONTAINS MORE THAN ONE OR TWO
MOLECULES. THERE ARE NO PROBLEMS TO CALCULATE ONE MOLECUL. IS IT POSSIBL
TO SEND ME A STREAM FILE?
WITH REGARD,
BEATE WOSNIK
From THOEFFEL@ELINET1.DOWELANCO.COM Mon May 3 09:11:06 1993
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Date: Mon, 3 May 1993 8:02:37 -0500 (EST)
From: THOEFFEL@ELINET1.DOWELANCO.COM
To: mytest
Message-Id: <930503080237.667@ELINET1.DOWELANCO.COM>
Subject: next test (test #2)
test DISTRIBUTED message.
thomas
From THOEFFEL@ELINET1.DOWELANCO.COM Mon May 3 09:17:19 1993
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Date: Mon, 3 May 1993 8:09:06 -0500 (EST)
From: THOEFFEL@ELINET1.DOWELANCO.COM
To: mytest
Message-Id: <930503080906.667@ELINET1.DOWELANCO.COM>
ljahdfjhasfjhasdfkjhalkf
;jaadfhashjkjhsdfkjhasdfhj
test for NO SUBJECT field
klsdfkjdfgkjsfdfdg
;skjdfgkjsdf;gkjsd;fkj
;skjdfglkjsdf;gkjsdfk
;ksjfdkjdfg;kjsdfg;kjsdg
;ldl;kfglkjsdfljsdfg;kj
;skdfjljsdf;kjsdfkl;skjfd
that should do it
thomas
From rossi@watson.ibm.com Mon May 3 12:13:30 1993
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id AA38168; Mon, 3 May 1993 12:10:03 -0400
Message-Id: <9305031610.AA38168@sandcastle.watson.ibm.com>
To: mytest
Subject: This is Test2
Date: Mon, 03 May 93 12:10:02 -0500
From: "Angelo R. Rossi (914-945-2834)" <rossi@watson.ibm.com>
Hello:
This is test 2. This is TEST two. This is definitely TEST TWO.
A. R. Rossi
From DEERFIELD@B.PSC.EDU Mon May 3 13:18:40 1993
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Date: Mon, 3 May 1993 13:15:07 -0400 (EDT)
From: DEERFIELD@B.PSC.EDU
To: mytest
Cc: DEERFIELD@B.PSC.EDU
Message-Id: <930503131507.20802da1@B.PSC.EDU>
test for NO SUBJECT field
Have received posts from:
Robert B. Funchess bobf@msi.com
Bruce tidor@mycroft.wi.mit.edu
Djamal Bouzida db3q@engcd.bu.edu
Boryeu Mao /PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/
ADMD=TELEMAIL/C=US/@sprint.com
Brian W. Beck F0388913@jaguar.csc.wsu.edu
Arne Elofsson arne@mango.mef.ki.se
Eldbjoerg Sofie Heimstad eldbjorg@chem.uit.no
Angelo R. Rossi rossi@watson.ibm.com
From DEERFIELD@B.PSC.EDU Mon May 3 13:20:06 1993
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Date: Mon, 3 May 1993 13:16:40 -0400 (EDT)
From: DEERFIELD@B.PSC.EDU
To: mytest
Message-Id: <930503131640.20802da1@B.PSC.EDU>
Subject: test2
test DISTRIBUTED message
Have received posts from:
Robert B. Funchess bobf@msi.com
Bruce tidor@mycroft.wi.mit.edu
Djamal Bouzida db3q@engcd.bu.edu
Boryeu Mao /PN=BORYEU.MAO/DD.ID=SSW.BMAO/PRMD=UPJOHN/
ADMD=TELEMAIL/C=US/@sprint.com
Brian W. Beck F0388913@jaguar.csc.wsu.edu
Arne Elofsson arne@mango.mef.ki.se
Eldbjoerg Sofie Heimstad eldbjorg@chem.uit.no
Angelo R. Rossi rossi@watson.ibm.com
Message without subject line:
** MESSAGE REJECTED BY: mytest@emperor.harvard.edu
David Deerfield deerfiel@psc.edu
From ryszard@MSI.COM Mon May 3 13:53:41 1993
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Date: Mon, 3 May 1993 13:49:55 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9305031749.AA01600@hogan.MSI.COM>
To: mytest%emperor@harvard
"test for NO SUBJECT field"
123456789 123456789 123456789 123456789 123456789
123456789 123456789 123456789 123456789 123456789
123456789 123456789 123456789 123456789 123456789
Hopefuly it has more then 100 characters,
Ryszard Czerminski, MSI
From ryszard@MSI.COM Mon May 3 14:00:46 1993
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Date: Mon, 3 May 1993 13:57:05 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9305031757.AA15437@hogan.MSI.COM>
To: mytest
Subject: test2
" test DISTRIBUTED message"
So far (Mon May 3 13:53:41 EDT 1993) I have received
5 messages. I have promptly deleted all of them so
I cannot from whom. More or less (in random order) from:
bobf
tidor
rossi
eldbjorg
<I do not remember>
It seems to work so far.
Ryszard Czerminski, MSI
From marc@david.saclay.cea.fr Tue May 4 09:08:18 1993
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X400-Received: by /PRMD=cicb/ADMD=atlas/C=FR/;
Relayed; 04 May 93 15:02:18+0200
X400-Received: by /PRMD=cea/ADMD=atlas/C=FR/;
Relayed; 04 May 93 20:06:14-0500
Date: 04 May 93 20:06:14-0500
From: SBPM Marc GINGOLD <marc@david.saclay.cea.fr>
Message-Id: <9305041906.AA03570(a)david.saclay.cea.fr>
To: mytest
test DISTRIBUTED message
Our Lan was down for some days.
Here is the reply
test DISTRIBUTED message from marc.
From marc@david.saclay.cea.fr Tue May 4 09:11:20 1993
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X400-Received: by /PRMD=cicb/ADMD=atlas/C=FR/;
Relayed; 04 May 93 15:05:26+0200
X400-Received: by /PRMD=cea/ADMD=atlas/C=FR/;
Relayed; 04 May 93 20:09:18-0500
Date: 04 May 93 20:09:18-0500
From: SBPM Marc GINGOLD <marc@david.saclay.cea.fr>
Message-Id: <9305041909.AA03643(a)david.saclay.cea.fr>
To: mytest
Subject: test DISTRIBUTED message
Our Lan was down for some days. We receive after returning to normal
activity several test messages. Including these of mytest-request
bbs is very useful. I post again my request: Is there an
install.com devoted to HP ? or a machdep.f ?
Bye!
This was a test DISTRIBUTED message from marc.
From dchin Wed May 5 14:35:52 1993
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Date: Wed, 5 May 93 14:35:52 -0400
From: dchin (Donovan Chin)
Message-Id: <9305051835.AA11207@emperor.harvard.edu>
To: charmm-bbs
Subject: ** Down Time.
Dear subscrbers of charmm-bbs.
I have been informed that the power to our chemistry building will be down
from 8:00 pm tonight (wednesday 5th) till late thursday afternoon (6 th).
Therefore, charmm-bbs will not be operating during this time.
Regards, Donovan
charmm-bbs-administrator.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
Donovan Chin Phone: 617.496.6820
Fax: 617.495.9857
Harvard University e-mail dchin@emperor.harvard.edu
Department of Chemistry
12 Oxford St.
Cambridge, MA 02138, USA
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=--=-=-=-=-=-=-=-=
END --> chmbbs-apr93.log <---
BEGIN --> may93.log <---
MAY93.log
--
From dchin Mon May 17 17:05:47 1993
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id AA11313; Mon, 17 May 93 17:05:47 -0400
Date: Mon, 17 May 93 17:05:47 -0400
From: dchin (Donovan Chin)
Message-Id: <9305172105.AA11313@emperor.harvard.edu>
To: charmm-bbs
Subject: ** NEW CHARMM-BBS **
** Attention charmm-bbs subscribers **
The new version of the charmm-bbs is now online.
*First let me give due credit.
Many thanks to all of you for taking part in the test
of the new charmm-bbs2.0. Many thanks Jan for help in
putting this together.
Here are the highlights of the new charmm-bbs(2.0):
What has NOT changed:
^^^^^^^^^^^^^^^^^^^^^
(1) The address is still "charmm-bbs@emperor.harvard.edu".
charmm-bbs-sysop@emperor.harvard.edu for subscription
info, list of subscribers etc...
(2) Messages posted to charmm-bbs are still archived on a
monthly basis. You can request these log files by sending
a message to 'charmm-bbs-sysop@emperor.harvard.edu'.
What HAS changed in the new charmm-bbs:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
(1) You will now get a confirmation e-mail message stating that
your message was accepted and will be distributed to charmm-bbs.
(2) Messages sent to charmm-bbs are pre-processed to determine if
they are acceptable and, if so, redirected to all the subscribers.
The main criteria for acceptability is as follows:
a. Returned mail is trapped by charmm-bbs2.0 (e.g. if a
person's address is no longer valid or a machine is down
somewhere). It is sent to charmm-bbs-administrator.
b. Charmm-bbs2.0 now requires that you use the 'Subject'
field. If you do not use the Subject field, it will send a
message back to you stating why you need to use the Subject
field along with your original message.
c. If there are any key words such as "subscribe,
please, add, remove, delete, drop" in the body of the message
AND the body of text is less than 100 characters; then it is
redirected to the charmm-bbs-administrator as it is probably
related to a subscription status.
d. If the body of the text is less than 100 characters and
doesn't contain one of the keywords in (c), then it is sent
to charmm-bbs-administrator. This may be contain words not
acceptable for distribution to the list. NOTE: if the body
of text contains personal signatures as well, it is possible
that one line messages could go to the list.
e. If the message is greater than 50 Kb it is rejected.
Once a message has been accepted by the charmm-bbs2.0 pre-
processor it will redirect to the list of subscribers.
When you see this message you will have an idea on what the
new distributed charmm-bbs2.0 mail will look like.
** A NOTE ON GENERAL POLICY **
** Many of you have expressed satisfaction with this bbs, which is good.
However, I would like to suggest a general policy that should be
applicable to all subscribers. I would like everyone who receives
responses to their posted questions, to post a summary of these responses
back to charmm-bbs. This will reduce any redundancies and may even
spark further discussions/questions on related topics.
** This bulletin board was created by :Donovan Chin:, it is not
sponsored by MSI or Harvard (although many members of MSI and the
Harvard community do participate). I only hope it serves some
purpose in bringing about the general useability of charmm
to a broader level.
If you have any questions on the above, please let me know.
Regards,
Donovan Chin
charmm-bbs-administrator
-------------------------------------------------------------------
DONOVAN CHIN Harvard University
E-mail: dchin@emperor.harvard.edu Department of Chemistry
Phone: (617) 495-9435 12 Oxford St.
Fax: (617) 495-9857 Cambridge, MA 02138, USA
-------------------------------------------------------------------
From brian@opus.chem.psu.edu Wed May 19 11:35:46 1993
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Date: Wed, 19 May 1993 11:32:28 -0400
From: brian@opus.chem.psu.edu (Brian J. Toleno)
Message-Id: <9305191532.AA15783@opus.chem.psu.edu>
To: charmm-bbs
Subject: A few questions
How can you delete more than one fragment at a time?
How can you change the number of waters of solvation in a solvation shell?
We are using the old Quanta. Thanks.
BT
brian@opus.chem.psu.edu
From MEMMS@CUNYVM.CUNY.EDU Thu May 20 17:35:54 1993
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Date: Thu, 20 May 93 17:26:46 EDT
From: Mihaly Mezei <MEMMS@cunyvm>
Subject: Null nonbonded group?
To: Charmm bb <charmm-bbs>
Hi,
we are getting the message
***** LEVEL -3 WARNING FROM <PARRDR> *****
***** Null nonbond group found. Redo.
while reading a parameter file. What does it mean and which part of the
parameter file does it come from?
This message comes after several
NOTE: atom type "MNA " is removed from previous group
type messages, but we got these notes earlier also without anything
untoward happening.
Thanks,
Mihaly Mezei
Mount Sinai School of MEdicine, CUNY
MEMMS@CUNYVM.CUNY.EDU
From stroop@chemie.fu-berlin.de Fri May 21 04:41:21 1993
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From: stroop@chemie.fu-berlin.de (Ralf Stroop)
Subject: Multiple Terms for Dihedrals
To: charmm-bbs%emperor@harvard
Date: Fri, 21 May 1993 10:36:41 +0100 (MES)
Cc: stroop@chemie.fu-berlin.de (Ralf Stroop)
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Hi,
Running CHARMm22 or MSI-CHARMm I usually get
warnings caused by 'multiple terms for dihedrals',
and in those cases that the multiple terms are
having the same periodicity I even get an ERROR:
PARRDR> Multiple terms for dihedral type CT -CT -CT -OE
PARRDR> ...
PARRDR> Error: Repeated TORSION parameter: INDEX 405 CODE25071790
PERIODICITY 1
* What is the purpos of having different multiple terms
for dihedrals (with different periodicities)?
* What's the way, CHARMm extract the right periodicity out
of the parameter-file?
Extract from the parameter-file:
...
CT CT CT OE 0.55 1 0.0
OE CT CT CT 0.69 1 0.0
...
CT CUA1 CUA1 CT 0.56 1 0.0
CT CUA1 CUA1 CT 3.45 2 180.0
...
CH2E CUA1 CUA1 CH2E 0.56 1 0.0
CH2E CUA1 CUA1 CH2E 3.45 2 180.0
...
CT CUA2 CUA2 CT 0.56 1 0.0
CT CUA2 CUA2 CT 3.45 2 180.0
...
CT CUA3 CUA3 CT 0.56 1 0.0
CT CUA3 CUA3 CT 3.45 2 180.0
...
(These messages don't appear running the same script
with CHARMm 21.3.)
Thanks in advance,
Ralf Stroop.
---------------------------------------------------------------
Ralf Stroop Werrastrasse 50 1000 Berlin 44 Germany
Tel.: +49/30/6874502 Email: stroop@chemie.fu-berlin.de
Freie Universitaet Berlin Institut fuer Kristallographie
Takustrasse 6 1000 Berlin 33 Tel.: +49/30/8382842
---------------------------------------------------------------
From ryszard@MSI.COM Tue May 25 13:15:05 1993
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From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9305251711.AA13105@hogan.MSI.COM>
To: charmm-bbs
Subject: Multiple Terms for Dihedrals
In response to Ralf Stroop question about dihedrals:
>>* What is the purpos of having different multiple terms
>> for dihedrals (with different periodicities)?
The purpose is to describe torsion potential more exactly.
Keep in mind that single sinusoid is only approximation to
the real (whatever it means) torsion potential. More exact
description of this potential can be made by using fourier
expansion (with different periodicities). Single sinusoid
is only first term of this expansion.
>>* What's the way, CHARMm extract the right periodicity out
>> of the parameter-file?
If there are two (or more - up to six) different periodicities
in parameter file, charmm is using all of them
e.g. in example below used potential would have a form
E(phi) = 0.56*(1+cos(phi)) + 3.45*(1+cos(2*phi+180))
>>CT CUA1 CUA1 CT 0.56 1 0.0
>>CT CUA1 CUA1 CT 3.45 2 180.0
>>CT CT CT OE 0.55 1 0.0
>>OE CT CT CT 0.69 1 0.0
Two lines above look like a bug in parameter file (e.g.
repeated torsion potential with different force constant )
From these lines you are getting an error message.
>>(These messages don't appear running the same script
>>with CHARMm 21.3.)
The reason for not getting these messages from charmm21.3
is the bug in charmm21.3, I believe. There was no checking
for multiple dihedrals and the last term from parameter
file was used.
Sincerely,
Ryszard Czerminski, MSI
From becky@MSI.COM Tue May 25 14:58:16 1993
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Date: Tue, 25 May 93 14:54:01 -0400
From: Becky Rone X 276 <becky@schizoid.MSI.COM>
To: charmm-bbs
Subject: dihedrals
The repeated dihedral was a bug in QUANTA 3.2 parameters for charmm21.3.
We now have a set of C-shells which sort parameters so that duplicates
can more easily be found. These shells were used in preparing QUANTA 3.3,
so this error does not appear in QUANTA 3.3.
END --> may93.log <---
BEGIN --> jun93.log <---
JUNE93.log
--
From MEMMS@CUNYVM.CUNY.EDU Thu Jun 3 17:29:01 1993
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Date: Thu, 03 Jun 93 17:23:50 EDT
From: Mihaly Mezei <MEMMS@cunyvm>
Subject: Null nonbonded group
To: Charmm bb <charmm-bbs>
Hi,
we were getting the message
***** LEVEL -3 WARNING FROM <PARRDR> *****
***** Null nonbond group found. Redo.
while reading a parameter file.
The message comes after several
NOTE: atom type "MNA " is removed from previous group
type messages, but we got these notes earlier also without anything
untoward happening.
Steve Fleischman told us that this indicates that a MASS statement
is missing from the RTF file.
I would be curious if someone knows the precise meaning if this message,
though.
Mihaly Mezei
Mount Sinai School of Medicine, CUNY
MEMMS@CUNYVM.CUNY.EDU
From brbrooks@helix.nih.gov Fri Jun 4 15:51:08 1993
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Date: Fri, 4 Jun 93 15:47:06 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9306041947.AA03816@helix.nih.gov>
To: MEMMS%cunyvm@harvard, charmm-bbs%emperor@harvard
Subject: Re: Null nonbonded group
Cc: brbrooks@helix.nih.gov
The meaning of the message "Null nonbond group found, redo."
is that there is a group of vdw atom types that has no members.
This can indicate a repeated atom type, or the establishemnt
of a wildcard group followed by a series of explicit removals
until the group is empty. In either case it indicates a potential
problem that should be fixed. The easiest fix is to comment out
the line which establishes the null group.
Bernie Brooks
From "PSI%SURFNET.1412007::GAIA::groot"@caos.caos.kun.nl Tue Jun 8 06:16:27 1993
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Date: Tue, 8 Jun 1993 12:09:21 METDST
From: "PSI%SURFNET.1412007::GAIA::groot"@caos.caos.kun.nl
Subject: modelling protein-peptide complexes
To: CHARMM-BBS
Message-Id: <01GZ4VJ2Y5WYA23H62@caos.caos.kun.nl>
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For some time I have been trying to model complexes between proteins and
oligopeptides. I use the default charged N- and C-terminal patches for
the peptides in combination with a distance dependent dielectric (including
explicit water molecules is not feasible because of the large amount
of peptides I want to study). However, interactions between the termini
of the peptide and the protein residues seem to unrealistically dominate
the binding. Does anybody recognize this problem? Does anybody has
suggestions for solving this problem ?
Peter Grootenhuis
--------------------------------------------------------------------------------
E-mail address: grootenhuis@akzo.akzo.400net.nl
==> The "reply" or "answer" commands will NOT work for answering this mail.
You need to specify the whole e-mail address.
Postal address:
Organon International bv --- Dr. Peter D.J. Grootenhuis --- CMC group KR1004
P.O. Box 20 --- 5340 BH OSS --- The Netherlands
Phone: 31-4120-61920 --- Fax: 31-4120-62539
--------------------------------------------------------------------------------
From JARRINM%AM.mrgate@woods.ulowell.edu Fri Jun 11 14:00:04 1993
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Date: Fri, 11 Jun 1993 13:55:57 EDT
From: JARRINM%AM.mrgate@woods.ulowell.edu
To: CHARMM-BBS
X-Vmsmail-To: CHARMM-BBS@EMPEROR.HARVARD.EDU
Message-Id: <0096DDE8.993A89E0.24682@woods.ulowell.edu>
Subject: Merging dynamics files
I am trying to merge different trajectories of dynamics into one.
For this I have tried to use the command MERGE, but with no succes so far.
I have not been able to write the correct CHARMm sript. Does anibody knows
how to do this? If so maybe you could share your script with us, or maybe
give me a few pointers. Thank you.
Mario Jarri'n
jarrinm@woods.ulowell.edu
From ryszard@MSI.COM Fri Jun 11 14:43:25 1993
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Date: Fri, 11 Jun 1993 14:39:13 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9306111839.AA14795@hogan.MSI.COM>
To: CHARMM-BBS%emperor@harvard, JARRINM%AM.mrgate@woods.ulowell.edu
Subject: Re: Merging dynamics files
In standard charmm package there is test directory.
Some of the files in this directory are using MERGE command
(dyntest1 dyntest2 quasi stdtest trnphi).
You may try to use them as an examples.
Ryszard Czerminski, MSI
From chind@cobalt.ulowell.edu Fri Jun 11 14:51:34 1993
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From: chind@cobalt.ulowell.edu
Message-Id: <9306111846.AA07958@cobalt.ulowell.edu>
To: CHARMM-BBS%emperor@harvard, JARRINM%AM.mrgate@woods.ulowell.edu
Subject: Re: Merging dynamics files
Try this...
...TOP OF CHARMM SCRIPT RTF'F ETC..
!Files i want to merge..
set 1 small
open read unit 23 file name @1_a1.dcd
open read unit 24 file name @1_a2.dcd
open read unit 25 file name @1_a3.dcd
open read unit 26 file name @1_a4.dcd
!Name of file i want to merge the above to...
open write unit 60 file name BIG_aa.dcd
!Now do merge command..
merge coor firstu 23 nunit 4 skip 1 nfile 40 outputu 60
stop
You will need to change nfile (number of records you expect in the output
file), nunit (the number of files you are merging), and maby skip
(number of records to skip in writing the output file). See the
documentation file dynamc.doc in the $CHM_DATA/doc directory for more
details..
--Donovan
From rita@black.sci.kun.nl Wed Jun 16 10:39:46 1993
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Message-Id: <199306161435.AA19800@wn1.sci.kun.nl>
To: charmm-bbs
Cc: rita@black.sci.kun.nl
Subject: Charmm crystal builder
Date: Wed, 16 Jun 93 16:35:35 +0200
From: rita@black.sci.kun.nl
Dear Mrs. and Mr.,
I am a student and I'm supposed to be working
with the Charmm crystal builder, but I bumped
into a fatal problem (help!):
I need to know the orientation of the
a-, b- and c-axes in the x, y, z carthesian coordinate system,
since this orientation defines the orientation of the
primary structure with respect to the a-, b- and c- axes
(which define the lattice).
Allmost every orientation of the primary structure in the same
lattice defines a different crystal structure, so I need the
information mentioned above to know which crystal structure
I am building. Unfortunately there is no documentation on this.
The Harvard documentation mentions that the convention used by
CHARMM for orientating the crystal in real space may be found in
the routine CONCOR in [.MANIP]CORMAN2.SRC, but I have no access
to Charmm source files.
Can someone out there please help me?
Thanks in advance,
Rita Bijlsma
......................
R. Bijlsma University of Nijmegen
e-mail: rita@sci.kun.nl
From ryszard@MSI.COM Wed Jun 16 15:31:46 1993
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Date: Wed, 16 Jun 1993 15:27:26 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9306161927.AA13469@hogan.MSI.COM>
To: charmm-bbs%emperor@harvard, rita@black.sci.kun.nl
Subject: Re: Charmm crystal builder
Please find enclosed fragment of corman.doc file which explains
the orientation of unit cell vectors (abc) with respect to
cartesian coordinate system (xyz).
Note that the described 'coordinate convert' command is new
and may not yet exists in the charmm which you have.
...
14) The CONVert command
The COOR CONVert command will cause the coordinates of all
defined and selected atoms to be transformed from the unit cell to
cartesian coordinates or back from cartesian to fractional coordinates.
Two orientations in cartesian coordinates are supported :
ALIGned - in which b-vector is along y-axis and a-vector
in xy-plane (this is old charmm standard)
SYMMetric - in which shape matrix constructed from unit
cell vectors is symmetric
Two keywords in any order [FRAC|ALIG|SYMM] are required after CONVert.
Unit cell parameters (a,b,c,alpha,beta,gamma) follow in the same line.
(NOTE: this is different!!!)
...
Ryszard Czerminski, MSI
From cqsimpson@halnet.com Wed Jun 16 18:37:27 1993
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Date: Wed, 16 Jun 1993 17:35:17 -0500
From: cqsimpson@halnet.com (Charlie Simpson)
Message-Id: <9306162235.AA12551@cre2>
To: charmm-bbs
Subject: request for charmm-bbs
Cc:
I would like to sign up for the CHARMM bbs. For what it's worth, Halliburton
Service leads the Oil Service industry and Oil Companies in the area of
Computational Chemistry/Molecular Modeling. We have very close ties with MSI
and IBM and would be glad to be a part of the charmm-bbs. Thus, if you're
looking for additional leading industrial charmm user groups, feel free to
use our name.
Regards,
================================================================================
Charlie Simpson Ph.D. cqsimpson@halnet.com
Halliburton Services
P.O. Box 1431 Phone 405/251-4564
Duncan, OK 73536-0444 Fax 405/251-3218
Life for him was an adventure, and perilous indeed, but men were not made for
safe havens.
-- Edith Hamilton on Aeschylus
================================================================================
From eldbjorg@chem.uit.no Thu Jun 17 07:32:14 1993
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Date: Thu, 17 Jun 93 13:32:12 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9306171332.AA04201@trypsin.chem.uit.no>
To: charmm-bbs
Subject: merge coor
I also have problems with merging trajectory files, have tried
with different values of "SKIP", but the same error message
remain unchanged. These two following files has different SKIP
values, is that really the problem!?
-elle.
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From eldbjorg@chem.uit.no Thu Jun 17 07:39:41 1993
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Date: Thu, 17 Jun 93 13:39:43 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9306171339.AA04225@trypsin.chem.uit.no>
To: charmm-bbs
Subject: merge error
Sorry, forgot the error message using "merge coor":
READING TRAJECTORY FROM UNIT 50
NUMBER OF COORDINATE SETS IN FILE: 100
NUMBER OF PREVIOUS DYNAMICS STEPS: 51000
FREQUENCY FOR SAVING COORDINATES: 1000
NUMBER OF STEPS FOR CREATION RUN: 100000
TITLE> * COORDINATES AFTER EQUILIBRATION DYNAMICS
TITLE> * DATE: 1/29/93 11:27:44 CREATED BY USER: eldbjorg
TITLE> *
***** WARNING ***** SKIP= 1 WAS NOT A MULTIPLE OF THE FILE INTERVAL= 1000
IT HAS BEEN RESET TO 1000
***** WARNING ***** BEGIN= 0 WAS NOT IN THE INPUT FILE
IT HAS BEEN RESET TO 51000
SKIP = 1000 NBEGN = 51000 NSTEP =100000 TRAJU= 60
VCLOSE: Closing unit 50 with status "KEEP"
100 COORDINATE SETS STARTING FROM
STEP NO 51000 FOR EVERY 1000 STEPS
WRITTEN ON UNIT 60
VCLOSE: Closing unit 60 with status "KEEP"
READING TRAJECTORY FROM UNIT 51
NUMBER OF COORDINATE SETS IN FILE: 100
NUMBER OF PREVIOUS DYNAMICS STEPS: 150500
FREQUENCY FOR SAVING COORDINATES: 500
NUMBER OF STEPS FOR CREATION RUN: 50000
***** ERROR ***** FILES DO NOT MERGE
UNIT 51 BEGINS AT 150500 INSTEAD OF 151000
*** LEVEL -1 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.
Execution terminated due to the detection of a fatal error.
-elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From @surrey.ac.uk,@central.surrey.ac.uk:chs1nt@surrey.ac.uk Thu Jun 17 11:40:58 1993
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Via: central.surrey.ac.uk; Thu, 17 Jun 93 15:15:06 BST
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From: Dr Nicholas P Tomkinson <chs1nt@surrey.ac.uk>
Message-Id: <9306171413.AA04331@central.surrey.ac.uk>
Subject: merge coor
To: charmm-bbs
Date: Thu, 17 Jun 93 15:13:45 BST
Mailer: Elm [revision: 66.25]
I have a similar problem with the traj read/write commands. I have previously
heated over 12500 steps and (stupidly probably but isn't hindsight a wonderful
thing) saved every 1000 steps in the consequent equilibration/simulation.
As a result I have a simulation that starts at step 23500 and has step
interval of 1000. If I try to read this it tells me that BEGIN = 23500 is not
a multiple of SKIP = 1000. OK, so I know that I should have perhaps used a
save of 500 steps or equilibrated for an extra 500 steps to make life easier,
but is there anything to do in retrospect or should I just redo the simulation?
Nick Tomkinson
From parasol@netcom.com Thu Jun 17 13:10:50 1993
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From: parasol@netcom.com (Shashi Raval)
Message-Id: <9306171707.AA10677@netcom4.netcom.com>
Subject: A faster version of CHARMM?
To: charmm-bbs
Date: Thu, 17 Jun 93 10:07:13 PDT
X-Mailer: ELM [version 2.3 PL11]
To all CHARMM users.
Parasol Inc. has been re-organizing CHARMM to develop a truly parallelized,
distributed implementation.
Key to our success is, of course, the even distribution of the atoms and
workload over the network of processors. This is dependent on the molecule,
its environment, and the way it is being manipulated. To further our
development, we would like to test our approach on real applications.
Parasol would like to hear from any users who:
- use large numbers of atoms,
- would benefit from substantial speed up in processing time, and
- would be prepared to share their scripts with us, so we
can investigate the potential for our approach.
If you are interested in helping, please contact
Peter Hunt parasol@netcom.com
Parasol inc. (408) 354 9525
--
From becky@MSI.COM Thu Jun 17 13:20:20 1993
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Date: Thu, 17 Jun 93 13:16:03 -0400
From: Becky Rone X 276 <becky@schizoid.MSI.COM>
To: charmm-bbs
Subject: merge and skip
For some of you having trouble the following explanation may help.
As I understand it the trajectory files actually store not the
originating frame, but the first stored frame. So if the first
calculation after a DYNA command is the 5000 step and you are
storing every 100th step, the first frame in the file is really
5100. Now I might be wrong about what I remember, but give it a try.
Furthermore, I never could merge two files which were saved at
different intervals. I heard that a few hardcore CHARMMites have
small pieces of code which can perform this action.
If you have QUANTA you might give it a chance.
As I recall you can read each file in the Conformatonal Search
trim the set to some interval which sets a common denominator and
perform the analysis on this consistent set.
If you don't have QUANTA the same logic may work. Write each
trajectory at a common denominator value using skip and then
merge the two files.
I also vaguely remember that in some spots the skip command
actually refers to the frame number not the step number at which
the coordinates were written.
Good Luck all.
From eldbjorg@chem.uit.no Fri Jun 18 10:10:13 1993
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Date: Fri, 18 Jun 93 16:10:21 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9306181610.AA05270@trypsin.chem.uit.no>
To: charmm-bbs
Subject: neutral
Cc: eldborg@chem.uit.no
I want to make the charges of acidic,
basic, N-termini and C-termini functional groups
net neutral. I have changed (in the PDB file)
to ARGN, ASPH, GLUH and LYSN, and tried to
model N-ter and C-ter in QUANTA, but get
unwanted positive charge on the protein.
Is there any better way to do this,
perhaps with CHARMM standalone?!
Thanks in advance,
-elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From ryszard@MSI.COM Fri Jun 18 10:33:13 1993
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Date: Fri, 18 Jun 1993 10:28:39 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9306181428.AA10557@hogan.MSI.COM>
To: charmm-bbs%emperor@harvard, eldbjorg@chem.uit.no
Subject: Re: neutral
Cc: eldborg@chem.uit.no
With charmm standalone you can modify charges using
scalar command (see scalar.doc).
For example to modify charge of the first atom to -0.76 you have to issue
following command
scalar charge set -0.76 sele bynu 1:1 end.
See also select.doc for examples how to use selection facility.
Ryszard Czerminski, MSI
From varma@sfu.ca Mon Jun 21 14:39:33 1993
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Date: Mon, 21 Jun 93 11:35:21 -0700
From: varma@sfu.ca
Message-Id: <9306211835.AA06889@beaufort.sfu.ca>
To: charmm-bbs
Subject: Dynamics
I have two questions concerning md simulations.
1) When running simulations in water, what is the average fluctuations
observed? I usually heat for 10,000 steps and equilibrate for the same
time, but always observe +/- 20 degree high low values from the intended
simulation temperature (300K).
2) this concerns quanta - Does Quanta produce a random SEED
when running dynamics -i.e., if you run two two dynamics, will you
observe different results, or will the trajectories be identical?
Thanks in advance
**************************************************
Vikram Varma
Dept. of Chemistry
Simon Fraser University
Burnaby, B.C. V5A 1S6.
Canada
Off (604) 291 5650
Fax (604) 291 3765
**************************************************
From "PSI%SURFNET.1412007::MOIRA::groot"@caos.caos.kun.nl Thu Jun 24 03:33:29 1993
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Date: Thu, 24 Jun 1993 09:24:59 METDST
From: "PSI%SURFNET.1412007::MOIRA::groot"@caos.caos.kun.nl
Subject: interaction function
To: CHARMM-BBS
Message-Id: <01GZR2GSOCV6AATYZT@caos.caos.kun.nl>
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Dear Netters,
I have a series of noncovalently bound enzyme-inhibitor complexes for which
the 3D-structures have been determined/modelled.
I am trying to find computational methods that will allow me to estimate
the binding between the enzyme and these inhibitors. In other words: does
somebody know of A VALIDATED (published) INTERACTION FUNCTION ? Are
there papers in which experimentally determined binding data are correlated
with calculated interaction energies?
Since I am interested in both a large number and a wide variety of inhibitor
structures I don't think free energy perturbation methods will help me with
respect to this.
Peter
Grootenhuis
--------------------------------------------------------------------------------
E-mail address: grootenhuis@akzo.akzo.400net.nl
==> The "reply" or "answer" commands will NOT work for answering this mail.
You need to specify the whole e-mail address.
Postal address:
Organon International bv --- Dr. Peter D.J. Grootenhuis --- CMC group KR1004
P.O. Box 20 --- 5340 BH OSS --- The Netherlands
Phone: 31-4120-61920 --- Fax: 31-4120-62539
--------------------------------------------------------------------------------
From belandrum@halnet.com Thu Jul 1 15:05:00 1993
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From: belandrum@halnet.com (Bruce E. Landrum)
Message-Id: <9307011855.AA19631@cre1>
To: CHARMM-bbs
Subject: subroutine to read DCDs
Cc:
I would like to be able to have a subroutine that I can read individual frames
from a dynamic DCD file so that I can perform specialized calculations. Does
anyone have such a subroutine developed already? If so, I would appreciate
receiving the source code to it.
Thanks,
Bruce
===============================================================================
Bruce E. Landrum blandrum@halnet.com
Halliburton Energy Services
P.O. Drawer 1431 Phone 405/251-4470
Duncan, OK 73536-0438 Fax 405/251-4155
===============================================================================
From becky@MSI.COM Thu Jul 1 16:07:08 1993
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Date: Thu, 1 Jul 93 16:01:34 -0400
From: Becky Rone X 276 <becky@schizoid.MSI.COM>
To: charmm-bbs
Subject: dynamics trajectories
Cc: support@seavoid.MSI.COM
Dear Bruce:
Take a look at the TRAJ READ command. It can be used very successfully to
process single frames in any manner you choose. You can even write
a user subroutine to perform the desired calculations on your molecule,
if CHARMm does not provide the capability you what. However, CHARMm is
overflowing with statistical capabilities to use on DYNAMICS. QUANTA
accesses only a part of all the things that CHARMm can do. But don't
overlook the analysis facility in QUANTA it can do a number of things
for the analysis of DYNAMIC trajectories in an easy and convenient
manner.
From burkhart@rds325.goodyear.com Thu Jul 1 17:13:38 1993
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Date: Thu, 1 Jul 93 17:07:36 -0400
From: burkhart@rds325.goodyear.com (Craig W. Burkhart)
Message-Id: <9307012107.AA18451@rds325>
To: charmm-bbs
Subject: DCD File Formats (and other stuff...)
Concerning the current round of talk on CHARMm .DCD files:
- Becky is right about the TRAJ facility. It can supply you with
an entire set I/O capabilities. CHARMm is full of correlation
capabilities. I use it to do velocity correlations for
molecular diffusion constants. It would not pay you to
write your own code to do something similar. Writing
a CHARMm script is much easier.
- The binary .DCD format is published in MSI's doc set.
See "Quanta User's Guide Supplement", Ch. 10, Part 4, pp. 155-6.
MSI's DCD documentation is a bit tricky to read though -- so be
careful.
I had a similar thing in mind, but I want to use Mathematica
to do the visualization. What I want is a 2D raster plot of
time on the x-axis and a set of torsions (from say a polymer
chain's backbone) on the y-axis. Each torsion would have
a time set of raster cells associated with it. The value of
a particular torsion would be color coded according to some
natural scheme (say, the Tektronix color wheel for hue). The
mapping would be done in a particular torsion's modulo 360 value.
Does anyone have a Mathematica package (or any other code)
to do this? Integral to this kind of visualization is
reading both .DCD, .PSF files and Quanta torsion family
(.tor) files. Fortunately, .PSFs and .tor are usually in ascii.
DCD files are a bit more problematic...
I was thinking about doing this in my spare time in the
near future. But if anyone has done it already, please
pass on the information.
--------------------------------------------------------------------------
Craig W. Burkhart, Ph.D The Goodyear Tire & Rubber Co.
Senior Research Chemist Akron Technical Center
E-mail: cburkhart@goodyear.com Akron, OH 44309-3531
Phone: 216.796.4431
Fax: 216.796.3947
--------------------------------------------------------------------------
From F0388913@JAGUAR.CSC.WSU.EDU Thu Jul 1 20:35:01 1993
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Date: Thu, 1 Jul 1993 17:30:43 -0700 (PDT)
From: "Brian W. Beck" <F0388913@JAGUAR.CSC.WSU.EDU>
To: charmm-bbs
Cc: F0388913@JAGUAR.CSC.WSU.EDU
Message-Id: <930701173043.230028c5@JAGUAR.CSC.WSU.EDU>
Subject: DCD file pseudo-code
Concerning the recent requests for code which reads
binary .DCD files, my group and I frequently do so
to generate g(r), elec-static-pot, etc data. Included
below is some pseudo-fortran-code which reasonably describes
the format of a .DCD file. I pretty much used this pseudo-code
to act as the kernel for my first .DCD reading program.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
------------------------------- CUT HERE --------------------------------------
parameter (nfrmax=500,ishmax=200,natmax=3000)
implicit real*8 (a-h,o-z)
character*4 hdr
character*4 endmark
character*80 title(20)
character*80 dcdfile
character*16 outfile
c in dcd files all the x,y,z are saved as real not real*8
c for charmm21
real*4 x(natmax),y(natmax),z(natmax)
real*4 blen,xij,yij,zij
integer ICNTRL(20)
c
read(5,*) dcdfile
open(20,file=dcdfile,form='unformatted')
c
c HDR for coordinate files is "CORD"
c HDR for velocity files is "VELD"
c icntrl(1)=NUMBER OF COORDINATE SETS IN FILE
c icntrl(2)=first step written
c icntrl(3)=FREQUENCY FOR SAVING COORDINATES
c icntrl(4)=NUMBER OF STEPS FOR CREATION RUN
c icntrl(5)=frequency for saving velocities
c icntrl(6)=0
c icntrl(7)=0
c icntrl(8)=number of degrees of freedom
c icntrl(9)=number of "fixed" atoms=0
c i10=number of lines in title
c all the titles start with "*"
c natrec=total number of atoms
c nfreat=natrec-icntrl(9)
c
hdr='CORD'
write(20) hdr,icntrl
write(20) i10,(title(j),j=1,i10)
write(20) natrec
natomT=natrec
nfix=icntrl(9)
natom=natomT-nfix
c iterating on time frames
do 180 iframe=1,numframe
if (iframe.eq.1) then
write(20) (x(i),i=1,natomT)
write(20) (y(i),i=1,natomT)
write(20) (z(i),i=1,natomT)
else
write(20) (x(i+nfix),i=1,natom)
write(20) (y(i+nfix),i=1,natom)
write(20) (z(i+nfix),i=1,natom)
endif
180 continue
stop
END
From laaksone@csc.fi Fri Jul 2 01:33:44 1993
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Date: Fri, 2 Jul 1993 08:27:43 +0300 (EET)
From: Leif Laaksonen <Leif.Laaksonen@csc.fi>
Subject: CHARMm binary DCD files
To: charmm-bbs%emperor@harvard
Message-Id: <Pine.3.07.9307020843.A16161-c100000@convex.csc.fi>
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Here is the "body" of a small fortran program I use when
I want to read a binary trajectory file. Observe, however,
that this code does not work for a constant pressure simulation
and there is no check for maximum number of atoms.
But it is possible to use it and add further code to it.
Cheers,
-leif laaksonen
---------------cut here----------------
C
C Small fortran program to scan the trajectory
C
C Leif laaksonen 1993
C
PARAMETER (MAXATOMS = 15000)
C
dimension x(MAXATOMS)
dimension y(MAXATOMS)
dimension z(MAXATOMS)
dimension icntrl(20)
character FileName*256
character hdr*4
character*80 title(32)
write(6,*) 'Give file name'
read(5,'(A)') FileName
open(unit = 21 , status = "OLD" , file = FileName ,
1 form="UNFORMATTED" , ERR = 100)
read(21) hdr,icntrl
write(6,'(a)') 'HDR is: ',hdr
write(6,*) 'Number of data sets: ',icntrl(1)
read(21) ntitl,(title(i),i=1,ntitl)
do i=1,ntitl
write(6,'(a)') title(i)
enddo
read(21) natom
write(6,*) 'Number of atoms: ',natom
nfreat = natom - icntrl(9)
write(6,*) 'Number of free atoms: ',nfreat
do 5 i=1,icntrl(1)
write(6,*) 'reading frame: ',i
if(i .eq. 1) then
read(21) (x(j),j=1,natom)
read(21) (x(j),j=1,natom)
read(21) (x(j),j=1,natom)
else
read(21) (x(j),j=1,nfreat)
read(21) (x(j),j=1,nfreat)
read(21) (x(j),j=1,nfreat)
endif
5 continue
stop
100 continue
write(6,*) 'Cant open input file properly'
end
---------------cut here----------------
-------------------------------------------------------------------
Leif Laaksonen |
Center for Scientific Computing | Phone: 358 0 4572378
P.O. Box 405 | Telefax: 358 0 4572302
FIN-02101 Espoo | Voice Mail: 358 486257407
FINLAND | Mail: Leif.Laaksonen@csc.fi
I need a fix 'cause I'm going down
Down to the bits that I left uptown
Lennon/McCartney
-------------------------------------------------------------------
END --> jun93.log <---
BEGIN --> jul93.log <---
JULY93.log
--
From belandrum@halnet.com Thu Jul 1 15:05:00 1993
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Date: Thu, 1 Jul 1993 13:55:13 -0500
From: belandrum@halnet.com (Bruce E. Landrum)
Message-Id: <9307011855.AA19631@cre1>
To: CHARMM-bbs
Subject: subroutine to read DCDs
Cc:
I would like to be able to have a subroutine that I can read individual frames
from a dynamic DCD file so that I can perform specialized calculations. Does
anyone have such a subroutine developed already? If so, I would appreciate
receiving the source code to it.
Thanks,
Bruce
===============================================================================
Bruce E. Landrum blandrum@halnet.com
Halliburton Energy Services
P.O. Drawer 1431 Phone 405/251-4470
Duncan, OK 73536-0438 Fax 405/251-4155
===============================================================================
From becky@MSI.COM Thu Jul 1 16:07:08 1993
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From: Becky Rone X 276 <becky@schizoid.MSI.COM>
To: charmm-bbs
Subject: dynamics trajectories
Cc: support@seavoid.MSI.COM
Dear Bruce:
Take a look at the TRAJ READ command. It can be used very successfully to
process single frames in any manner you choose. You can even write
a user subroutine to perform the desired calculations on your molecule,
if CHARMm does not provide the capability you what. However, CHARMm is
overflowing with statistical capabilities to use on DYNAMICS. QUANTA
accesses only a part of all the things that CHARMm can do. But don't
overlook the analysis facility in QUANTA it can do a number of things
for the analysis of DYNAMIC trajectories in an easy and convenient
manner.
From burkhart@rds325.goodyear.com Thu Jul 1 17:13:38 1993
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Date: Thu, 1 Jul 93 17:07:36 -0400
From: burkhart@rds325.goodyear.com (Craig W. Burkhart)
Message-Id: <9307012107.AA18451@rds325>
To: charmm-bbs
Subject: DCD File Formats (and other stuff...)
Concerning the current round of talk on CHARMm .DCD files:
- Becky is right about the TRAJ facility. It can supply you with
an entire set I/O capabilities. CHARMm is full of correlation
capabilities. I use it to do velocity correlations for
molecular diffusion constants. It would not pay you to
write your own code to do something similar. Writing
a CHARMm script is much easier.
- The binary .DCD format is published in MSI's doc set.
See "Quanta User's Guide Supplement", Ch. 10, Part 4, pp. 155-6.
MSI's DCD documentation is a bit tricky to read though -- so be
careful.
I had a similar thing in mind, but I want to use Mathematica
to do the visualization. What I want is a 2D raster plot of
time on the x-axis and a set of torsions (from say a polymer
chain's backbone) on the y-axis. Each torsion would have
a time set of raster cells associated with it. The value of
a particular torsion would be color coded according to some
natural scheme (say, the Tektronix color wheel for hue). The
mapping would be done in a particular torsion's modulo 360 value.
Does anyone have a Mathematica package (or any other code)
to do this? Integral to this kind of visualization is
reading both .DCD, .PSF files and Quanta torsion family
(.tor) files. Fortunately, .PSFs and .tor are usually in ascii.
DCD files are a bit more problematic...
I was thinking about doing this in my spare time in the
near future. But if anyone has done it already, please
pass on the information.
--------------------------------------------------------------------------
Craig W. Burkhart, Ph.D The Goodyear Tire & Rubber Co.
Senior Research Chemist Akron Technical Center
E-mail: cburkhart@goodyear.com Akron, OH 44309-3531
Phone: 216.796.4431
Fax: 216.796.3947
--------------------------------------------------------------------------
From F0388913@JAGUAR.CSC.WSU.EDU Thu Jul 1 20:35:01 1993
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Date: Thu, 1 Jul 1993 17:30:43 -0700 (PDT)
From: "Brian W. Beck" <F0388913@JAGUAR.CSC.WSU.EDU>
To: charmm-bbs
Cc: F0388913@JAGUAR.CSC.WSU.EDU
Message-Id: <930701173043.230028c5@JAGUAR.CSC.WSU.EDU>
Subject: DCD file pseudo-code
Concerning the recent requests for code which reads
binary .DCD files, my group and I frequently do so
to generate g(r), elec-static-pot, etc data. Included
below is some pseudo-fortran-code which reasonably describes
the format of a .DCD file. I pretty much used this pseudo-code
to act as the kernel for my first .DCD reading program.
-Brian
================================================================================
| Brian W. Beck | Disclaimer: WASHINGTON ST. UNIVERSITY is only |
|--------------------| responsible for the thoughts in my head. The |
| Biochem/Biophysics | gibberish that pours forth from my lips and |
| WSU , 261 Fulmer | fingertips is of no consequence and should |
| Pullman, WA 99164 | be ignored at all costs. |
| (509) 335 - 4083 | |
|--------------------------------------|---------------------------------------|
| E-mail Address: |Heisenberg's Molecular Voodoo Principle|
| INTERNET F0388913@jaguar.csc.wsu.edu |"If there's a CAAT in a Pribnow box, |
| BITNET F0388913@WSUVMS1 | you don't know whether it's "alive" |
| DECNET JAGUAR::F0388913 | and functioning until you look inside"|
================================================================================
------------------------------- CUT HERE --------------------------------------
parameter (nfrmax=500,ishmax=200,natmax=3000)
implicit real*8 (a-h,o-z)
character*4 hdr
character*4 endmark
character*80 title(20)
character*80 dcdfile
character*16 outfile
c in dcd files all the x,y,z are saved as real not real*8
c for charmm21
real*4 x(natmax),y(natmax),z(natmax)
real*4 blen,xij,yij,zij
integer ICNTRL(20)
c
read(5,*) dcdfile
open(20,file=dcdfile,form='unformatted')
c
c HDR for coordinate files is "CORD"
c HDR for velocity files is "VELD"
c icntrl(1)=NUMBER OF COORDINATE SETS IN FILE
c icntrl(2)=first step written
c icntrl(3)=FREQUENCY FOR SAVING COORDINATES
c icntrl(4)=NUMBER OF STEPS FOR CREATION RUN
c icntrl(5)=frequency for saving velocities
c icntrl(6)=0
c icntrl(7)=0
c icntrl(8)=number of degrees of freedom
c icntrl(9)=number of "fixed" atoms=0
c i10=number of lines in title
c all the titles start with "*"
c natrec=total number of atoms
c nfreat=natrec-icntrl(9)
c
hdr='CORD'
write(20) hdr,icntrl
write(20) i10,(title(j),j=1,i10)
write(20) natrec
natomT=natrec
nfix=icntrl(9)
natom=natomT-nfix
c iterating on time frames
do 180 iframe=1,numframe
if (iframe.eq.1) then
write(20) (x(i),i=1,natomT)
write(20) (y(i),i=1,natomT)
write(20) (z(i),i=1,natomT)
else
write(20) (x(i+nfix),i=1,natom)
write(20) (y(i+nfix),i=1,natom)
write(20) (z(i+nfix),i=1,natom)
endif
180 continue
stop
END
From laaksone@csc.fi Fri Jul 2 01:33:44 1993
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Date: Fri, 2 Jul 1993 08:27:43 +0300 (EET)
From: Leif Laaksonen <Leif.Laaksonen@csc.fi>
Subject: CHARMm binary DCD files
To: charmm-bbs%emperor@harvard
Message-Id: <Pine.3.07.9307020843.A16161-c100000@convex.csc.fi>
Mime-Version: 1.0
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Here is the "body" of a small fortran program I use when
I want to read a binary trajectory file. Observe, however,
that this code does not work for a constant pressure simulation
and there is no check for maximum number of atoms.
But it is possible to use it and add further code to it.
Cheers,
-leif laaksonen
---------------cut here----------------
C
C Small fortran program to scan the trajectory
C
C Leif laaksonen 1993
C
PARAMETER (MAXATOMS = 15000)
C
dimension x(MAXATOMS)
dimension y(MAXATOMS)
dimension z(MAXATOMS)
dimension icntrl(20)
character FileName*256
character hdr*4
character*80 title(32)
write(6,*) 'Give file name'
read(5,'(A)') FileName
open(unit = 21 , status = "OLD" , file = FileName ,
1 form="UNFORMATTED" , ERR = 100)
read(21) hdr,icntrl
write(6,'(a)') 'HDR is: ',hdr
write(6,*) 'Number of data sets: ',icntrl(1)
read(21) ntitl,(title(i),i=1,ntitl)
do i=1,ntitl
write(6,'(a)') title(i)
enddo
read(21) natom
write(6,*) 'Number of atoms: ',natom
nfreat = natom - icntrl(9)
write(6,*) 'Number of free atoms: ',nfreat
do 5 i=1,icntrl(1)
write(6,*) 'reading frame: ',i
if(i .eq. 1) then
read(21) (x(j),j=1,natom)
read(21) (x(j),j=1,natom)
read(21) (x(j),j=1,natom)
else
read(21) (x(j),j=1,nfreat)
read(21) (x(j),j=1,nfreat)
read(21) (x(j),j=1,nfreat)
endif
5 continue
stop
100 continue
write(6,*) 'Cant open input file properly'
end
---------------cut here----------------
-------------------------------------------------------------------
Leif Laaksonen |
Center for Scientific Computing | Phone: 358 0 4572378
P.O. Box 405 | Telefax: 358 0 4572302
FIN-02101 Espoo | Voice Mail: 358 486257407
FINLAND | Mail: Leif.Laaksonen@csc.fi
I need a fix 'cause I'm going down
Down to the bits that I left uptown
Lennon/McCartney
-------------------------------------------------------------------
From W.P.vanHoorn@ct.utwente.nl Tue Jul 6 11:49:41 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9307061641.AA06185@utctu6.ct.utwente.nl>
Subject: Calculating dihedral angles within CHARMm
To: charmm-bbs, quanta-l@msi.com
Date: Tue, 6 Jul 1993 17:41:11 +0000 (WDT)
X-Mailer: ELM [version 2.4 PL5]
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Dear Netters,
Does anyone know how to calculate -within charmm- dihedral angles? I
have a script that produces a lot of structures, so it is not possible
for me to calculate manually the dihedral angles with Quanta. In the
file miscom.doc I found the following reference:
Quick command substitution paramteters:
'XVAL' - X position of group of atoms
'YVAL' - X position of group of atoms
'ZVAL' - X position of group of atoms
'DIST' - Distance between two atom analysis
'THET' - Angle for three atom analysis
'PHI ' - Dihedral for four atom analysis
The 'PHI ' command seems the one I need, but I can't get it working
with ?phi substitutions.
Thanks in advance,
----------------------------------------------------------------------
(Ir.) Willem Paul van Hoorn
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (NL)53-892955
P.O. Box 217 (NL)53-892980
7500 AE Enschede, The Netherlands fax : (NL)53-356024
----------------------------------------------------------------------
From arne@mango.mef.ki.se Wed Jul 7 04:01:18 1993
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To: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Cc: charmm-bbs%emperor@harvard, quanta-l@msi.com, arne@mango.mef.ki.se
Subject: Re: Calculating dihedral angles within CHARMm
In-Reply-To: (Your message of Tue, 06 Jul 93 17:41:11 GMT.)
<9307061641.AA06185@utctu6.ct.utwente.nl>
Date: Wed, 07 Jul 93 09:56:29 +0000
From: 'Arne Elofsson (arne@mango.mef.ki.se)' <arne@mango.mef.ki.se>
The best way to do this (if there are many structures)
is to put all coordinates into a trajectory
and then use correl.
I think you also might try to use IC (intcor) it should work
I think.
arne
PS. I have a flex (or fortran) file that puts a number
of files into a trajectory. (if you are interested)
From Don_Gregory@MSI.COM Wed Jul 7 14:33:59 1993
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Date: 7 Jul 1993 14:28:51 +0000
From: "Don Gregory" <Don_Gregory@MSI.COM>
Subject: contouring surfaces
To: "CHARMM BBS" <charmm-bbs>, "Quanta BBS" <quanta-l@MSI.COM>
Subject: Time:2:17 PM
OFFICE MEMO contouring surfaces Date:7/7/93
There's been some interesting discussion recently
regarding how to contour properties on the surface
of molecules within Quanta; with some excellent
suggestions given by Bruce Bush at Merck.
Anyone interested can also review a fortran
program written by Rod Hubbard, to do the same
kind of thing, but with respect to a number of
interesting properties. The program is still somewhat
under development, but the full source code, and
include files are available in
$QNT_ROOT/user_group_files/Hubbard.92-06-22
and the program name is "proprty.f"
When you run this program, you supply an msf name,
a parameter file name ($HYD_LIB/param.par) a
grid step size, and an 'option'.
Try this and see what you think. It would be quite
useful to get some feedback as to the properties
users would like to see included, not only in a
program of this nature, but when such functionality
is to be added to Quanta in the future, what
capabilities would be of greatest use.
Don Gregory
Mgr. Appl. Sci. MSI
From GRIMB@caos.caos.kun.nl Thu Jul 8 05:48:04 1993
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Date: Thu, 8 Jul 1993 11:40:56 METDST
From: GRIMB@caos.caos.kun.nl
Subject: image keywords
To: charmm-bbs%emperor@harvard
Message-Id: <01H0AR81YS76AC2Z04@caos.caos.kun.nl>
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Hello,
I have some problems with the image specs keywords. I can't find information
about the INVErse and NOINVerse keywords in the CHARMm manual or the
documents. Can somebody explain the function of these keywords to me?
Reinier Grimbergen
-----------------------------------------------------------------------------
RIM Labatory of Solid State Chemistry
University of Nijmegen
Toernooiveld
6525 ED Nijmegen
The Netherlands
-----------------------------------------------------------------------------
From ryszard@MSI.COM Fri Jul 9 10:43:07 1993
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Date: Fri, 9 Jul 1993 10:38:39 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9307091438.AA14978@hogan.MSI.COM>
To: charmm-bbs
Subject: hexagonal water box
Does anybody have a way to construct, with charmm,
hexagonal water box which would be useful for DNA hydration
(or even better, ready charmm script to do just that ?)
All hints will be highly appreciated.
Ryszard Czerminski, MSI
From burkhart@goodyear.com Fri Jul 9 11:10:18 1993
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Date: Fri, 9 Jul 93 11:04:03 -0400
From: burkhart@goodyear.com (Craig W. Burkhart)
Message-Id: <9307091504.AA25953@rds325>
To: charmm-bbs
Subject: Hexagonal Water Box
I'm not sure about what is meant by a hexagonal water box. Do
you mean a monoclinic unit cell with the setting angle = 120.0 degrees?
If so, then this would not be any different than setting up a solvent
box with a cubic cell. Just set your box with the crystal parameters,
set the molecules in the box, and do the standard minimization and
equilibrations with the periodic boundary conditions...
Does that answer your question?
--------------------------------------------------------------------------
Craig W. Burkhart, Ph.D The Goodyear Tire & Rubber Co.
Senior Research Chemist Akron Technical Center
E-mail: cburkhart@goodyear.com Akron, OH 44309-3531
Fone: 216.796.4431
Fax: 216.796.3947
--------------------------------------------------------------------------
"For a successful technology, reality must take precedence over
public relations, for Nature cannot be fooled"
- Feynman
--------------------------------------------------------------------------
From burkhart@goodyear.com Fri Jul 9 13:30:18 1993
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Date: Fri, 9 Jul 93 13:24:07 -0400
From: burkhart@goodyear.com (Craig W. Burkhart)
Message-Id: <9307091724.AA26446@rds325>
To: charmm-bbs
Subject: Free Energies of Solvation
I am in need of calculating the free energy of solvation for a
two-molecule complex in the presence of a hydrocarbon solvent.
What is the best way of computing the free energy. If someone
is an expert in perturbation and/or thermodynamic integration,
could you possibly send me an example CHARMm script -- or
a stepwise approach to writing the script?
Thanks.
--------------------------------------------------------------------------
Craig W. Burkhart, Ph.D The Goodyear Tire & Rubber Co.
Senior Research Chemist Akron Technical Center
E-mail: cburkhart@goodyear.com Akron, OH 44309-3531
Fone: 216.796.4431
Fax: 216.796.3947
--------------------------------------------------------------------------
"For a successful technology, reality must take precedence over
public relations, for Nature cannot be fooled"
- Feynman
--------------------------------------------------------------------------
From wahle@mace.cc.purdue.edu Tue Jul 13 15:53:01 1993
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Date: Tue, 13 Jul 93 14:48:32 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9307131948.AA29602@mace.cc.purdue.edu>
To: charmm-bbs
Subject: Extracting atomic coordinates from CHARMm images
I need to know whether I can get the atomic coordinates from images
created in CHARMm. I have created a crystal lattice using CHARMm images
with the CRYSTAL DEFINE and CRYSTAL READ commands. After the lattice is
formed and some atoms on the real residue are rotated, I calculate the
energy and minimize the entire lattice, images included. What I need to
do is get the atomic coordinates from the images after the minimization.
Right now all I get are the atomic coordinates from the real residue. I
have talked with people at MSI who help with Quanta problems, but they
are unaware of a way to do this in CHARMm. The only way they know how to
do it is if I retain the copies when I exit from the crystal builder. I am
running all of these commands in a CHARMm script file.
Any help received is greatly appreciated!
Mark C. Wahle
Department of Medicinal Chemistry
Purdue University
e-mail : wahle@mace.cc.purdue.edu
From raman@bioc01.uthscsa.edu Tue Jul 13 17:22:42 1993
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From: raman@bioc01.uthscsa.edu (C.S.RAMAN)
Message-Id: <9307132118.AA09113@bioc01.uthscsa.edu>
Subject: GROMOS
To: charmm-bbs
Date: Tue, 13 Jul 1993 16:18:46 -0500 (CDT)
X-Mailer: ELM [version 2.4 PL3]
Content-Type: text
Content-Length: 992
Hi
Is anyone aware of a mailing list like this one for the users of the
program GROMOS? I have an email address to obtain the distribution but
none for a listserv! Any information regarding this would be highly
appreciated!
Thanks
-raman
--
C.S.Raman raman@bioc01.uthscsa.edu - Internet
UNIX Programming & Administration 70412.2354@compuserve.com - CIS
SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC
Department of Biochemistry craman@launchpad.unc.edu
UTHSCSA
7703 Floyd Curl Dr. (210) 567-6623 [Tel]
San Antonio, TX 78284-7760 (210) 567-6595 [Fax]
******************************************************************************
If a man's wit be wandering, let him study the Mathematics
-Francis Bacon
******************************************************************************
From bobf@MSI.COM Tue Jul 13 17:34:18 1993
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From: Bob Funchess <bobf@MSI.COM>
Date: Tue, 13 Jul 1993 17:29:27 -0400
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: charmm-bbs
Subject: Coordinates of image transformations
Depending on how one defines the images it is possible to get the coordinates
of any given transformation. The commands to use are a combination of COOR
OPER and PRINT COOR. The following example assumes the P-1 space group.
CRYS DEFI TRICLINIC 10.0 10.0 10.0 90.0 90.0 90.0
READ IMAGE CARD INIT FREE
* IMAGE TRANSFORMATIONS
*
IMAGE X
IMAGE XNEG
NEGA X
END
COOR OPER XNEG SELE ALL END
PRINT COOR
If you wanted to do several transforms you could set up some sort of loop and
use COOR COPY / COOR COPY COMP to restore the 'original' coordinates in
between the transformations.
Bob Funchess
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Technical Support Scientist 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From dchin Tue Jul 13 17:57:27 1993
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Date: Tue, 13 Jul 93 17:57:27 -0400
From: dchin (Donovan Chin)
Message-Id: <9307132157.AA18035@emperor.harvard.edu>
To: charmm-bbs
Subject: writing xtal coor.
A simple way to write out coor of the transformations
of a asymetric unit is to type:
{assuming you have generated the neccessary images}
update imgfrq 20 cutim 999.0 imgfrq 20
open write unit 9 card name @2_img.crd
write coor image unit 9 card
* img
*
It is important to have used "update imgfrq 20 cutim 999.0 imgfrq 20"
as this keys the "write coor image" to do just that.
--D
-------------------------------------------------------------------
DONOVAN CHIN Harvard University
E-mail: dchin@emperor.harvard.edu Department of Chemistry
Phone: (617) 495-9435 12 Oxford St.
Fax: (617) 495-9857 Cambridge, MA 02138, USA
-------------------------------------------------------------------
From becky@MSI.COM Tue Jul 13 19:39:46 1993
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From: Becky Rone X 276 <becky@schizoid.MSI.COM>
To: charmm-bbs
Subject: images
Try WRITE COOR ..... IMAGES. I think that will do it.
From wahle@mace.cc.purdue.edu Wed Jul 14 12:23:22 1993
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Date: Wed, 14 Jul 93 11:18:49 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9307141618.AA00922@mace.cc.purdue.edu>
To: charmm-bbs
Subject: CHARMm Images thanks
To all who sent in answer to my CHARMm crystal images question, thank you.
I am presently attempting to change my script file to include the suggestions
made by various individuals. I will inform you on how it works out. Due to
my present schedule, it may not be until next week, but stay tuned. (Sorry
for the incorrect English above.)
Mark C. Wahle
Deparment of Medicinal Chemistry
Purdue University
E-mail: wahle@mace.cc.purdue.edu
From MEMMS@CUNYVM.CUNY.EDU Thu Jul 15 17:11:45 1993
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Date: Thu, 15 Jul 93 17:00:23 EDT
From: Mihaly Mezei <MEMMS@cunyvm>
Subject: RTF angles
To: CHARMM BB <charmm-bbs>
We generated an alpha helix (phi=-61 deg, psi=-41.6 deg, omega= 180 deg)
with Charmm, using the new and old RTF's. Using the new, however, gave a
structure, that, once brought up in Quanta, did not have the proper
hydrogen-bond pattern.
Upon inspection of the RTF's, it seems that the old RFT was AUTOGENERATing
the angles, while the new gave them explicitely with IC statements, and as
such, thes should indeed be 'better'.
So, the question is, how does one generate a decent alpha helix with the new
RTF, one that has the hydrogen bonds we all read about in the textbooks?
Mihaly Mezei
Mount Sinai School of Medicine, CUNY
From benhamou@lynx.dac.neu.edu Fri Jul 16 16:32:42 1993
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Subject: subscribe
To: charmm-bbs
Date: Fri, 16 Jul 93 16:27:05 EDT
From: Said Benhamou <benhamou@lynx.dac.neu.edu>
Cc: benhamou@lynx.dac.neu.edu (Said Benhamou)
X-Mailer: ELM [version 2.3 PL11]
Subscribe
To whom it may concern,
Please subscribe me to this group.
Thank you very much.
-- o__
Said Benhamou _.>/ _
E-Mail: benhamou@lynx.dac.neu.edu (_) \(_)
From tennant%hau410.uk.smithkline.com@smithkline.com Tue Jul 20 05:16:38 1993
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Date: Tue, 20 Jul 1993 10:04:27 +0100 (BST)
From: Mike Tennant <tennant%hau410.uk.smithkline.com@smithkline.com>
Subject: harmonic constraints
To: Charmm Bulletin Board <charmm-bbs%emperor@harvard>
Message-Id: <Pine.3.05.9307201027.E2692-b100000@hau410.uk.smithkline.com>
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Hi All,
Can anybody help me with a quick question? If one uses the
comparison coordinates to constrain atoms with the cons harm keyword, does
running dynamics simulations overwrite the constraints (ie when the
velocities are written to the comparison coords). If so, is there any way
around this? Any answers would be most appreciated!
cheers,
Mike.
_____________________________________________________________________________
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Coldharbour Rd |
| | |___ \\|_| | || Harlow |
| \____ \ | _ < || Essex |
| ___| | | |_| | || CM19 5AD |
| \_____/ |____/ || England |
| || Harlow (0279) 622000x3328 |
|_____________________________________________________________________________|
| Mike Tennant |
| Email: tennant%hau410.uk.smithkline.com@phinet.smithkline.com |
|*****************************************************************************|
| God is real, unless declared integer.
------------------------------------------------------------------------------|
From eldbjorg@chem.uit.no Tue Jul 20 09:18:14 1993
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Date: Tue, 20 Jul 93 15:18:55 GMT
From: eldbjorg@chem.uit.no
Message-Id: <9307201518.AA02153@trypsin.chem.uit.no>
To: charmm-bbs
Subject: PDB format
Cc: eldbjorg@chem.uit.no
Has anyone experienced problem with reading
PDB files created by "FRODO" or "CHAIN" in CHARMm?
Thanks in advance,
elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From mitchell_t%frgen.dnet@smithkline.com Tue Jul 20 10:42:04 1993
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Date: Tue, 20 Jul 93 10:29:27 -0400
Message-Id: <9307201429.AA26880@smithkline.com>
From: mitchell_t%frgen.dnet@smithkline.com
To: charmm_bbs@smithkline.com.local
Subject: RE: pdb from FRODO
Re: Reading in FRODO PDB files...
Check that FRODO writes out the segid in cols 73-76. This is non-
standard pdb, but CHARMm insists on it.
If this is the problem......
Try importing into Quanta (I'm assuming you have it!) and exporting
as a "CHARMm/XPLOR pdb" file.
If you are a unix user, I have a csh/awk script to format and "ordinary"
pdb file for use with CHARMm. I can put in on the net if anyone is
interested.
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax. (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || mitchell_t%frgen.dnet@smithkline.com U.K. |
-------------------------------------------------------------------------------
--end--
-------------------------------------------------------------------
DONOVAN CHIN Harvard University
E-mail: dchin@emperor.harvard.edu Department of Chemistry
Phone: (617) 495-9435 12 Oxford St.
Fax: (617) 495-9857 Cambridge, MA 02138, USA
-------------------------------------------------------------------
From belandrum@halnet.com Tue Jul 20 11:52:22 1993
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Date: Tue, 20 Jul 1993 10:41:25 -0500
From: belandrum@halnet.com (Bruce E. Landrum)
Message-Id: <9307201541.AA16808@cre1>
To: CHARMM-bbs
Subject: scripts, etc.
Cc:
The awk script sounds like the type of thing that MSI should be encouraging
their users to provide to their bbs for ftp. That way users don't have to
reinvent the wheel.
===============================================================================
Bruce E. Landrum blandrum@halnet.com
Halliburton Energy Services
P.O. Drawer 1431 Phone 405/251-4470
Duncan, OK 73536-0438 Fax 405/251-4155
===============================================================================
From mitchell_t%frgen.dnet@smithkline.com Wed Jul 21 05:29:29 1993
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Date: Wed, 21 Jul 93 05:13:55 -0400
Message-Id: <9307210913.AA05603@smithkline.com>
From: mitchell_t%frgen.dnet@smithkline.com
To: charmm_bbs@smithkline.com.local
Subject: csh and awk scripts for CHARMm pdb files
#
# A csh procedure to convert pdb files into something CHARMm will like
# Usage: pdb_charmm filespec
# Where filespec is the pdb files to be re-formatted.
# Wildcards etc. can be used
# re-formatted files haver their root names upper-cased
#
# For a small molecule, will set the segid to the resname
# optionally, if the resid does not start at one, the output file
# can be written with the (first) resid as one.
# If there are different residues in the file, the segid will be set to
# SEG1, though I guess it would be easy enough to prompt for it
#
# Enjoy !! (and if any *real* unix weenies want to "perfect"
# the scripts, please send me a copy !)
#
# T. Mitchell Feb 1993 mitchell_t%frgen.dnet@smithkline.com
#
echo -n "Enter a target directory (<CR> for current) > "
set temp = ($<)
setenv tdir $temp
if (`printenv tdir` == "") then
echo "CHARMm format pdb files -> "$cwd
else
setenv tdir $tdir"/"
echo "CHARMm format pdb files -> "$tdir
endif
set file1 = $1
set rec1 = (`cut -f1 -d" " $file1`)
set resid = (`cut -c18-21 $file1`)
set resno = (`cut -c25-26 $file1`)
echo rec1 is $rec1[1]
echo resid is $resid[1]
echo resno is $resno[1]
set ans = ""
if ($resno[1] != 1) then
echo "The residue no. does not start at 1,"
echo -n "Do you want to renumber all residues to 1 (y/n) [y] > "
set ans = $<
if ($ans != "n") set ans = "y"
endif
set count = 0
set segid = $resid[1]
foreach r($rec1)
echo count r $count $r
echo "resid(count) $resid[$count]"
@ count ++
if ( $r == "TER" || $r == "CONECT" ) then
echo TER or CONECT found
break
else if ($count > 1 && $r == "ATOM") then
if ($prev != $resid[$count])then
echo "Resids are different, segid set to SEG1"
set segid = SEG1
break
endif
endif
set prev = $resid[$count]
end
echo segid $segid
foreach i($argv)
if (! -r $i) then
echo $i not found
continue
endif
setenv ext $i:e
setenv root $i:r
setenv ucroot `echo $root | tr '[a-z]' '[A-Z]'`
echo $tdir$ucroot'.'$ext
if ($ans == "y") then
nawk -f /usr/scripts/awk2_pdb $i > $tdir$ucroot'.'$ext
else if ($segid == "") then
nawk -f /usr/scripts/awk_pdb $i > $tdir$ucroot'.'$ext
else
nawk -f /usr/scripts/awk1_pdb $i > $tdir$ucroot'.'$ext
endif
end
#[End of pdb_charmm]
# Here are the awk scripts -- you will have to extract them to files
# awk_pdb, awk1_pdb, awk2_pdb respectively.
# I can't remember why there should be different scripts, and they
# look to be the same for me, but it seems to work OK!
# awk_pdb
{ if ($1 == "ATOM")
printf ("%4s%7d %4-s %4-s%5d %8.3f%8.3f%8.3f%18s%4-s\n", \
$1,$2," "$3,$4,"1",$6,$7,$8," ",$4)
else
print $0 }
# awk1_pdb
{ if ($1 == "ATOM")
printf ("%4s%7d %4-s %4-s%5d %8.3f%8.3f%8.3f%18s%4-s\n", \
$1,$2," "$3,$4,"1",$6,$7,$8," ",$4)
else
print $0 }
# awk2_pdb
{ if ($1 == "ATOM")
printf ("%4s%7d %4-s %4-s%5d %8.3f%8.3f%8.3f%18s%4-s\n", \
$1,$2," "$3,$4,"1",$6,$7,$8," ",$4)
else
print $0 }
From YAMAMURA%CGF@Arizona.edu Wed Jul 21 16:25:46 1993
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<01H0T082R59SA8C2S0@Arizona.edu>; Wed, 21 Jul 1993 13:20:58 MST
Date: Wed, 21 Jul 1993 13:20:58 -0700 (MST)
From: YAMAMURA%CGF@Arizona.edu
Subject: Looking for information on charmm on DEC alphas
To: charmm-bbs
Message-Id: <01H0T082TAFMA8C2S0@Arizona.edu>
X-Vms-To: @CHARMM.POST
X-Vms-Cc: YAMAMURA
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
Content-Transfer-Encoding: 7BIT
Does anyone out there know about the availability of charmm2X
on DEC alphas? If so, which operating system? (OPen VMS or OSF/1).
Would an alpha 3000 model 300 with monochrome monitor and 32 mb of memory
support charmm2X if the implementation exists or is an implementation
being considered for the near future? WOuld really appreciate hearing
what you know about these questions.
Responses can be send directly to
yamamura@cgf.chem.Arizona.EDU
and I will summarize back to the list.
Thanks very much.
Susan Yamamura
From mitchell_t%frgen.dnet@smithkline.com Fri Jul 23 04:44:17 1993
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Date: Fri, 23 Jul 93 04:25:32 -0400
Message-Id: <9307230825.AA27838@smithkline.com>
From: mitchell_t%frgen.dnet@smithkline.com
To: charmm_bbs@smithkline.com.local
Subject: PDB --> CHARMm PDB format
#
# Ooops, A couple of goofs in the last file I sent ( in the awk scripts)
# This should fix it -- apologies for any inconvenience.
#
# A csh procedure to convert pdb files into something CHARMm will like
# Usage: pdb_charmm filespec
# Where filespec is the pdb files to be re-formatted.
# Wildcards etc. can be used
# re-formatted files haver their root names upper-cased
#
# For a small molecule, will set the segid to the resname
# optionally, if the resid does not start at one, the output file
# can be written withe the (first) resid as one.
# If there are different residues in the file, the segid will be set to
# SEG1, though I guess it would be easy enough to prompt for it
#
# Enjoy !! -- and if any *real* unix weenies want to enhance
# this script -- send me a copy !
#
# T. Mitchell Feb 1993 mitchell_t%frgen.dnet%smithkline.com
#
echo -n "Enter a target directory (<CR> for current) > "
set temp = ($<)
setenv tdir $temp
if (`printenv tdir` == "") then
echo "CHARMm format pdb files -> "$cwd
else
setenv tdir $tdir"/"
echo "CHARMm format pdb files -> "$tdir
endif
set file1 = $1
set rec1 = (`cut -f1 -d" " $file1`)
set resid = (`cut -c18-21 $file1`)
set resno = (`cut -c25-26 $file1`)
echo rec1 is $rec1[1]
echo resid is $resid[1]
echo resno is $resno[1]
set ans = ""
if ($resno[1] != 1) then
echo "The residue no. does not start at 1,"
echo -n "Do you want to renumber all residues to 1 (y/n) [y] > "
set ans = $<
if ($ans != "n") set ans = "y"
endif
set count = 0
set segid = $resid[1]
foreach r($rec1)
echo count r $count $r
echo "resid(count) $resid[$count]"
@ count ++
if ( $r == "TER" || $r == "CONECT" ) then
echo TER or CONECT found
break
else if ($count > 1 && $r == "ATOM") then
if ($prev != $resid[$count])then
echo "Resids are different, segid set to SEG1"
set segid = SEG1
break
endif
endif
set prev = $resid[$count]
end
echo segid $segid
foreach i($argv)
if (! -r $i) then
echo $i not found
continue
endif
setenv ext $i:e
setenv root $i:r
setenv ucroot `echo $root | tr '[a-z]' '[A-Z]'`
echo $tdir$ucroot'.'$ext
if ($ans == "y") then
nawk -f awk2_pdb $i > $tdir$ucroot'.'$ext
else if ($segid == "") then
nawk -f awk_pdb $i > $tdir$ucroot'.'$ext
else
nawk -f awk1_pdb $i > $tdir$ucroot'.'$ext
endif
end
#[End of pdb_charmm]
# Here are the awk scripts -- you will have to extract them to files
# awk_pdb, awk1_pdb, awk2_pdb respectively.
# awk_pdb -- resid and sedid from input file
{ if ($1 == "ATOM")
printf ("%4s%7d%1s%4-s %4-s%5d %8.3f%8.3f%8.3f%18s%4-s\n", \
$1,$2," "$3,$4,$5,$6,$7,$8," ",$4)
else
print $0 }
#[end of awk_pdb]
# awk1_pdb -- resid from input file, segid --> SEG1
{ if ($1 == "ATOM")
printf ("%4s%7d%1s%4-s %4-s%5d %8.3f%8.3f%8.3f%18s%4-s\n", \
$1,$2," ",$3,$4,$5,$6,$7,$8," ","SEG1")
else
print $0 }
#[end of awk1_pdb]
# awk2_pdb -- resid --> 1, segid from input file
{ if ($1 == "ATOM")
printf ("%4s%7d%1s%4-s %4-s%5d %8.3f%8.3f%8.3f%18s%4-s\n", \
$1,$2," "$3,$4,"1",$6,$7,$8," ",$4)
else
print $0 }
#[end of awk2_pdb]
#[EOF]
From mitchell_t%frgen.dnet@smithkline.com Mon Jul 26 04:54:14 1993
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Date: Mon, 26 Jul 93 04:16:48 -0400
Message-Id: <9307260816.AA21409@smithkline.com>
From: mitchell_t%frgen.dnet@smithkline.com
To: charmm_bbs@smithkline.com.local
Subject: Stirring MSI into action
I've noticed with interest the complaints about MSI documentation --
which I whole-heartedly agree with. A secondary question also seemed to
be posed -- how do we get MSI to make these changes.
May I suggest to users in the US that they use their users group meeting
to shout loudly for improvements. In the UK, the MSI users group
meetings are often lively and vocal events (particularly after a c**p release)
-- Jeff Arnold (ex Polygen CEO) once turned up wearing a tee-shirt with
a target logo on it!. My understanding is that US meetings are more
subdued in comparison. MSI claim that they benefit from the UK
meetings because they get to hear users true feelings. We (the UK
users) get a chance to present a united front on what's wrong with
Quanta/CHARMm. Sometimes MSI even do something about it!. So come on
guys -- if you've got a problem, let 'em have it!!.
Tim Mitchell, Sec. UK MSI users group.
PS - Other European users. Any comments about your users group
meetings would be very interesting.
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax. (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || mitchell_t%frgen.dnet@smithkline.com U.K. |
-------------------------------------------------------------------------------
From robert@sg1.oc.wau.nl Mon Jul 26 10:06:28 1993
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Date: Mon, 26 Jul 93 14:59:20 GMT
From: robert@sg1.oc.wau.nl (Robert Schrijvers)
Message-Id: <9307261459.AA10608@Sg1.OC.wau.nl>
To: charmm-bbs
Subject: VIBRAN
Hi CHARMMERS
Does anyone has some suggestions on how to use the VIBRAN command on calculating
rotational barriers.
I calculated energy barriers by rotating (and constraining) the torsion angle
of interest step by step. I wonder if someone knows or uses a smart strategy
to analyse the highest energy structure wether this is the energy maximum as
a funtion of the rotating torsion angle or not.
Thanks in advance
Robert Schrijvers
Molecular Modeling & Design
Department of Organic Chemistry
Agricultural University Wageningen
Dreijenplein 8 6703 HB Wageningen
The Netherlands
Phone: 08370-82364
FAX:08370-84914
e-mail: robert@SG1.OC.WAU.NL
From ryszard@MSI.COM Mon Jul 26 15:33:21 1993
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Date: Mon, 26 Jul 1993 15:27:37 -0400
From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9307261927.AA14735@hogan.MSI.COM>
To: charmm-bbs%emperor@harvard, robert@sg1.oc.wau.nl
Subject: Re: VIBRAN
You may consider using TRAVEL facility
in CHARMM to calculate reaction paths.
If you have already your candidates for saddle points
and you want to make sure that these are realy saddle
points (i.e. there is only ONE normal mode with imaginary
frequency) then calculating frequencies with vibran should
be helpful.
Ryszard Czerminski, MSI
From peter@msi.ch Thu Jul 29 03:47:23 1993
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Date: Thu, 29 Jul 93 09:41:38 +0200
From: peter@msi.ch
Message-Id: <9307290741.AA14326@msi.ch>
To: charmm-bbs
Hello everybody,
I am looking for publications where CHARMm was
used to study sulfonamides. I would appreciate
to get some references.
Thank's for your help.
Peter Zbinden, MSI
e-mail: peter@msi.ch
From peter@msi.ch Thu Jul 29 03:56:29 1993
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Date: Thu, 29 Jul 93 09:50:59 +0200
From: peter@msi.ch
Message-Id: <9307290750.AA14470@msi.ch>
To: charmm-bbs
Subject: Sulfonamides
Hello everybody,
I am looking for publications where CHARMm was
used to study sulfonamides. I would appreciate
to get some references.
Thank's for your help.
Peter Zbinden, MSI
e-mail: peter@msi.ch
From tom@radical.chm.jhu.edu Fri Jul 30 11:51:29 1993
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Date: Fri, 30 Jul 93 11:38:38 -0400
From: tom@radical.chm.jhu.edu (Tom Tullius)
Sender: tom@radical.chm.jhu.edu
To: charmm-bbs
Subject: Constraints on nucleotide bases
To the Charmm bbs:
I am trying to "mutate" a DNA sequence by editing the resids in Quanta.
This works OK, but I would then like to minimize the new base. I have
had difficulty in writing a CHARMM command to constrain all the atoms of the
DNA other than the "mutant" base - this would include the deoxyribose and
the phosphate. Could someone give me a suggestion on how to simply
constrain only part of a residue (just the sugar and phosphate, not the
base)?
Cheers,
Tom
-------------------------------------------------------------------
Tom Tullius | tom@radical.chm.jhu.edu
Department of Chemistry | Telephone: (410) 516-7449
The Johns Hopkins University | FAX: (410) 516-8468
Baltimore, MD 21218 | [alternate FAX: (410) 516-5199]
From brbrooks@helix.nih.gov Thu Aug 5 23:26:22 1993
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From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9308060321.AA00506@helix.nih.gov>
To: GRIMB@caos.caos.kun.nl, charmm-bbs%emperor@harvard
Subject: Re: image keywords
The INVErse and NOINverse keywords in the image code are there for
debugging purposes. The NOINverse keyword allows Newton's third
law to be violated. If you are having trouble with the Image code,
these keywords will not help you.
Bernie Brooks
From brbrooks@helix.nih.gov Thu Aug 5 23:50:40 1993
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Date: Thu, 5 Aug 93 23:45:47 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9308060345.AA01692@helix.nih.gov>
To: YAMAMURA%CGF@Arizona.edu, charmm-bbs%emperor@harvard
Subject: Re: Looking for information on charmm on DEC alphas
We have CHARMM23 running well on a DEC alpha workstation under
OS/1. This is a supported machine with CHARMM23.
Bernie Brooks
From burkhart@goodyear.com Fri Aug 6 14:20:25 1993
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Date: Fri, 6 Aug 93 14:13:42 -0400
From: burkhart@goodyear.com (Craig W. Burkhart)
Message-Id: <9308061813.AA04583@rds325>
To: charmm-bbs, quanta-l@msi.com
Subject: Umbrella Sampling
Does anyone know if you can use a dummy atom as
a defined point in the reaction coordinate procedures
within CHARMm?
It looks like it is doubtful, as the dummy atoms
(at least when Quanta sets it up) have a different
syntax. Moreover, they don't show up when you do
a listing of the atoms.
If you cannot use dummy atoms, can anyone tell
me how to set up an equivalent point (that is,
a midpoint between two other atoms) as an
entity that RXNCord can use for a reaction coordinate?
--------------------------------------------------------------------------
Craig W. Burkhart, Ph.D Senior Research Chemist
E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co.
Fone: 216.796.4431 Akron Technical Center
Fax: 216.796.3947 Akron, OH 44309-3531
--------------------------------------------------------------------------
"Wine and friends must be old to be appreciated"
- old Italian maxim
--------------------------------------------------------------------------
From schaad@scsun.unige.ch Tue Aug 10 05:19:18 1993
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Date: Tue, 10 Aug 1993 11:04:09 +0200
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From: Schaad Olivier <schaad@scsun.unige.ch>
Message-Id: <243*/S=schaad/OU=scsun/O=unige/PRMD=switch/ADMD=arcom/C=ch/@MHS>
To: charmm-bbs
In-Reply-To: <9308091535.AA18593@emperor.harvard.edu>
Subject: Parameters for organic molecules
Dear sirs
I would like to add to the parameter version 22 from Harward University
the parameter for organic molecules like Pyridine, benzene, di-pyridine,
methyl, ether, esther, and Metal- Nitrogen.
Does anybody known a reference about using CHARMM with organic molecules,
especially parameters.
Thank
Olivier Schaad
-------------------------------------------------------------------
Olivier SCHAAD Geneva University
E-mail: schaad@scsun.unige.ch Department of Biochemistry-SCIENCES-II
Phone: (xx41 22) 702 6478 30, quai E-Ansermet
Fax: (xx41 22) 702 6476 Geneva, Switzerland Ch-1211
-------------------------------------------------------------------
From schaad@scsun.unige.ch Tue Aug 10 05:19:19 1993
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Date: Tue, 10 Aug 1993 11:09:13 +0200
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From: Schaad Olivier <schaad@scsun.unige.ch>
Message-Id: <244*/S=schaad/OU=scsun/O=unige/PRMD=switch/ADMD=arcom/C=ch/@MHS>
To: charmm-bbs
In-Reply-To: <9308091535.AA18593@emperor.harvard.edu>
Subject: Molecules sitting on axis of symetry
Dear sirs,
I would like to use the IMAGE facility in CHARMM and simulate
with symetry restraint a molecule with a internal symmetry like
Adamantane or benzene 1,5 di pyridine, or hb with water molecules around the
protein
Thank
Olivier Schaad
-------------------------------------------------------------------
Olivier SCHAAD Geneva University
E-mail: schaad@scsun.unige.ch Department of Biochemistry-SCIENCES-II
Phone: (xx41 22) 702 6478 30, quai E-Ansermet
Fax: (xx41 22) 702 6476 Geneva, Switzerland Ch-1211
-------------------------------------------------------------------
From luca@aeolus.ethz.ch Sat Aug 14 08:55:17 1993
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From: Luca Toldo <luca@aeolus.ethz.ch>
Message-Id: <10*/S=luca/OU=aeolus/O=ethz/PRMD=switch/ADMD=arcom/C=ch/@MHS>
To: charmm-bbs
Subject: CHARMM OPLS for Ammonium Sulphate and Ammonium Acetate ?
Dear Sirs, I wish to know which are the best OPLS parameters to
use for Ammonium Sulphate and for Ammonium Acetate.
Looking forward Your reply
LUCA TOLDO
SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZUERICH
email:Luca@aeolus.ethz.ch
From JARRINM%AM.mrgate@woods.ulowell.edu Sat Aug 14 16:52:53 1993
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Date: Sat, 14 Aug 1993 16:47:13 EDT
From: JARRINM%AM.mrgate@woods.ulowell.edu
To: CHARMM-BBS
X-Vmsmail-To: CHARMM-BBS@EMPEROR.HARVARD.EDU
Message-Id: <0097104B.20420BE0.23273@woods.ulowell.edu>
Subject: Correlation functions
When calculating correlation functions using CHARMm, there are a
few functions to choose from. One of this is called FFT. Can somebody tell me
what is the mathematical fuction FFT stands for?
Also when calculating spectral densities, there are four keywords
to choose from: [SIZE integer] [FOLD] [RAMP] [SWITCH]. What do these keywords
define?
Thank you,
Mario Jarrin
Chemisty Dpt
U. of MA at Lowell
Lowell, MA 01854
e-mail: jarrinm@woods.ulowell.edu
From tennant%hau410.uk.smithkline.com@smithkline.com Fri Aug 20 09:56:10 1993
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Date: Fri, 20 Aug 1993 14:45:04 +0100 (BST)
From: Mike Tennant <tennant%hau410.uk.smithkline.com@smithkline.com>
Subject: Dynamics
To: Charmm Bulletin Board <charmm-bbs%emperor@harvard>
Message-Id: <Pine.3.05.9308201404.W17263-b100000@hau410.uk.smithkline.com>
Mime-Version: 1.0
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Hi all,
Can anybody help with this one...? In a dynamics script, is iasors
0 meant to switch off the use of iasvel and just use iscvel, or does it
use a combination of both? The documentation implies (states) that
just the scaling option will be used, but in practice iasvel seems to be
independant of iasors. Any ideas?
cheers,
Mike.
_____________________________________________________________________________
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Coldharbour Rd |
| | |___ \\|_| | || Harlow |
| \____ \ | _ < || Essex |
| ___| | | |_| | || CM19 5AD |
| \_____/ |____/ || England |
| || Harlow (0279) 622000x3328 |
|_________________________________||__________________________________________|
| |
| Mike Tennant |
| Email: tennant%hau410.uk.smithkline.com@phinet.smithkline.com |
|*****************************************************************************|
| Save the Whales -- Harpoon a Honda. |
-------------------------------------------------------------------------------
From schaad@scsun.unige.ch Fri Aug 27 07:44:20 1993
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Date: Fri, 27 Aug 1993 13:38:37 +0200
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From: Schaad Olivier <schaad@scsun.unige.ch>
Message-Id: <298*/S=schaad/OU=scsun/O=unige/PRMD=switch/ADMD=arcom/C=ch/@MHS>
To: charmm-bbs
In-Reply-To: <9308091535.AA18593@emperor.harvard.edu>
Subject: Generate ALL angles and Dihedrals after a PATCH
Dear sirs
Do you known if it is possible to USE the Auto generate Angle and
dihedrals facility after a PATCH.
I would like to Create a new bond between to residues and then generate all
the Angle and Dihedrals and to be sure I am consistent with the
Energy function.
Thank
Olivier Schaad
-------------------------------------------------------------------
Olivier SCHAAD Geneva University
E-mail: schaad@scsun.unige.ch Department of Biochemistry-SCIENCES-II
Phone: (xx41 22) 702 6478 30, quai E-Ansermet
Fax: (xx41 22) 702 6476 Geneva, Switzerland Ch-1211
-------------------------------------------------------------------
From ln@pike.csb.ki.se Fri Aug 27 08:32:06 1993
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To: Schaad Olivier <schaad@scsun.unige.ch>
Cc: charmm-bbs%emperor@harvard
Subject: Re: Generate ALL angles and Dihedrals after a PATCH
In-Reply-To: (Your message of Fri, 27 Aug 93 13:38:37 O.)
<298*/S=schaad/OU=scsun/O=unige/PRMD=switch/ADMD=arcom/C=ch/@MHS>
Date: Fri, 27 Aug 93 14:25:14 +0100
From: "Lennart Nilsson, KI/CSB" <ln@pike.csb.ki.se>
the autogenerate facility does not apply to patches, meaning
that you have to include all relevant angles and dihedrals in the
patch residue definition in the rtf.
lennart nilsson
From brbrooks@helix.nih.gov Fri Aug 27 16:32:51 1993
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Date: Fri, 27 Aug 93 16:27:34 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9308272027.AA19352@helix.nih.gov>
To: charmm-bbs%emperor@harvard, schaad@scsun.unige.ch
Subject: Re: Generate ALL angles and Dihedrals after a PATCH
There is no facility to autogenerate after a patch. This is something
thatt we have wanted for some time, but no one has bothered to write the code.
Bernie Brooks
From silva@yang.mayo.EDU Fri Aug 27 16:44:24 1993
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Date: Fri, 27 Aug 93 15:37:03 -0500
From: silva@yang.mayo.EDU (Norberto Silva)
Message-Id: <9308272037.AA09616@yang.mayo.edu>
To: charmm-bbs
Subject: Stochastic boundary simulations
Hello,
I was wondering if someone would be kind enough to give an example
input file for doing a stochastic boundary simulation. I would also
appreciate if the person donating the input file would also put in a
couple of comments here and there so as to explain why certain
commands or parameter values were chosen in the simulation (I'll
understand though if this is asking for too much). I have already done
a lot of conformational searches with CHARMM as well as a little bit
of dynamics simulation on a whole protein. Thank you.
----------------------------------------------------------------------
Norberto D. Silva, Jr. "Superstition brings bad luck"
Mayo Clinic, Guggenheim 14 --Raymond Smullyan, 5000 B.C.
200 First St. SW
Rochester, MN 55905
FAX: (507) 284-9349
e-mail: silva@mayo.edu phone: (507) 284-5794
----------------------------------------------------------------------
From db3q@engcd.bu.edu Fri Aug 27 17:35:07 1993
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Date: Fri, 27 Aug 93 17:33:38 -0400
From: db3q@engcd.bu.edu (Djamal Bouzida)
Message-Id: <9308272133.AA02136@engcd.bu.edu.bu.edu>
To: CHARMM-bbs
Subject: CHARMM / Monte Carlo
I am writing this message to address the issue of the use of
Monte Carlo methods for studying equilibrium properties of
molecular systems. Many existing packages, including CHARMM,
do not have an option that the user could click to run a
Monte Carlo simulation on the system. Since I've dealt with
the efficiency and the flexibility of such methods during my
PhD thesis, and developed optimized MC methods, I've decided
to find a way on how to connect my routines with the CHARMM
code. The easiest solution I came up with was to link my main
program through the USER routine provided, and then call the
"rebuilding" and "energy-related" routines (SEED,BILDC,GETE,EPROP)
from within my program to rebuild the trial configuration and
update the MC-step. As you may already have guessed, this
procedure is very slow. The reason being that if the trial move
consists of moving only some part of the molecule (say a side
chain), the building routine will have to rebuild the whole
molecule, and the energy routine calculates the new energy of
the whole molecule also. And, since this is repeated many times,
it is very time consuming.
What I need is to rebuild only the new conformation of the
atoms that are moved, and the corresponding energy CHANGE
which is needed for the Metropolis updating process.
Could someone familiar with the routines above please let
me know whether it is possible to do what I described, and
thus increase the efficiency of the code. If yes, please
let me know how. If not, then what COMMON variables are needed
to rebuild only one part of the molecule within CHARMM and
computing the corresponding energy change.
PS: I have another technical request: I believe it should be
possible to call C routines through USER (Calling C from Fortran).
If someone has already done it, I would appreciate receiving a
sample of your code dealing with the interface. ThanQ.
--
Djamal Bouzida E-mail: db3q@engcd.bu.edu
From W.P.vanHoorn@ct.utwente.nl Mon Aug 30 09:27:02 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9308301417.AA16177@utctu6.ct.utwente.nl>
Subject: Re: CHARMM / Monte Carlo
To: charmm-bbs (CHARMm BBS)
Date: Mon, 30 Aug 1993 15:16:59 +0000 (WDT)
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Djamal Bouzida writes:
> Many existing packages, including CHARMM,
> do not have an option that the user could click to run a
> Monte Carlo simulation on the system. Since I've dealt with
> the efficiency and the flexibility of such methods during my
> PhD thesis, and developed optimized MC methods, I've decided
> to find a way on how to connect my routines with the CHARMM
> code.
I am very interested in using Monte Carlo within CHARMM. I notice
that 'life-science people' often use Molecular Dynamics, and
'material-science people' use Monte Carlo methods. Is their a
special reason for this? Or am I wrong about this?
(My PhD research consists of a material science subject: self
assembling organic monolayers, and I use the 'life science' program
Quanta/CHARMm, due to historic reasons).
Willem Paul
----------------------------------------------------------------------
(ir) Willem Paul van Hoorn
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (+31)53-892955
P.O. Box 217 (+31)53-892980
7500 AE Enschede, The Netherlands fax : (+31)53-356024
----------------------------------------------------------------------
From kreidler@convex.rz.uni-duesseldorf.de Tue Aug 31 11:51:15 1993
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From: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
Message-Id: <9308311546.AA28723@convex.rz.uni-duesseldorf.de>
Subject: h-bridges in CHARMM 22.0
To: charmm-bbs%emperor@harvard (charmm bbs)
Date: Tue, 31 Aug 1993 17:46:02 +0200 (MET)
Cc: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
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Hi folks out there!
I just read a paper of Milne et al. (J. Mol. Struct. 291, (1993) pp89-103
about "Molecular modeling in solvent". There it is described, that in CHARMM
version 21.2 the calculation of an explicit hydrogen bond term is not possible.
Is this feature implemented in later versions. At the Dept. of Inorganic
chemistry we use Charmm 3.3, which is version 22.0.
Thanx
Kay Kreidler
Dept. of Inorganic chemistry
Heinrich-Heine University Duesseldorf
Germany
From ln@pike.csb.ki.se Tue Sep 7 07:33:47 1993
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To: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
Cc: charmm-bbs%emperor@harvard (charmm bbs)
Subject: Re: h-bridges in CHARMM 22.0
In-Reply-To: (Your message of Tue, 31 Aug 93 17:46:02 O.)
<9308311546.AA28723@convex.rz.uni-duesseldorf.de>
Date: Tue, 07 Sep 93 13:26:39 +0100
From: "Lennart Nilsson, KI/CSB" <ln@pike.csb.ki.se>
the charmm energy function does contain a term for h-bonds; the current
parameterization, however, is made such that this term is not needed with
the coulomb and van der Waals terms taking up also the hbond energy.
a simple distance criterion is usually sufficient to determine if a hydrogen
bond is present or not.
lennart nilsson
END --> jul93.log <---
BEGIN --> aug93.log <---
AUG93.log
--
From brbrooks@helix.nih.gov Thu Aug 5 23:26:22 1993
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Date: Thu, 5 Aug 93 23:21:14 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9308060321.AA00506@helix.nih.gov>
To: GRIMB@caos.caos.kun.nl, charmm-bbs%emperor@harvard
Subject: Re: image keywords
The INVErse and NOINverse keywords in the image code are there for
debugging purposes. The NOINverse keyword allows Newton's third
law to be violated. If you are having trouble with the Image code,
these keywords will not help you.
Bernie Brooks
From brbrooks@helix.nih.gov Thu Aug 5 23:50:40 1993
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Date: Thu, 5 Aug 93 23:45:47 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9308060345.AA01692@helix.nih.gov>
To: YAMAMURA%CGF@Arizona.edu, charmm-bbs%emperor@harvard
Subject: Re: Looking for information on charmm on DEC alphas
We have CHARMM23 running well on a DEC alpha workstation under
OS/1. This is a supported machine with CHARMM23.
Bernie Brooks
From burkhart@goodyear.com Fri Aug 6 14:20:25 1993
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Date: Fri, 6 Aug 93 14:13:42 -0400
From: burkhart@goodyear.com (Craig W. Burkhart)
Message-Id: <9308061813.AA04583@rds325>
To: charmm-bbs, quanta-l@msi.com
Subject: Umbrella Sampling
Does anyone know if you can use a dummy atom as
a defined point in the reaction coordinate procedures
within CHARMm?
It looks like it is doubtful, as the dummy atoms
(at least when Quanta sets it up) have a different
syntax. Moreover, they don't show up when you do
a listing of the atoms.
If you cannot use dummy atoms, can anyone tell
me how to set up an equivalent point (that is,
a midpoint between two other atoms) as an
entity that RXNCord can use for a reaction coordinate?
--------------------------------------------------------------------------
Craig W. Burkhart, Ph.D Senior Research Chemist
E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co.
Fone: 216.796.4431 Akron Technical Center
Fax: 216.796.3947 Akron, OH 44309-3531
--------------------------------------------------------------------------
"Wine and friends must be old to be appreciated"
- old Italian maxim
--------------------------------------------------------------------------
From schaad@scsun.unige.ch Tue Aug 10 05:19:18 1993
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Date: Tue, 10 Aug 1993 11:04:09 +0200
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From: Schaad Olivier <schaad@scsun.unige.ch>
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To: charmm-bbs
In-Reply-To: <9308091535.AA18593@emperor.harvard.edu>
Subject: Parameters for organic molecules
Dear sirs
I would like to add to the parameter version 22 from Harward University
the parameter for organic molecules like Pyridine, benzene, di-pyridine,
methyl, ether, esther, and Metal- Nitrogen.
Does anybody known a reference about using CHARMM with organic molecules,
especially parameters.
Thank
Olivier Schaad
-------------------------------------------------------------------
Olivier SCHAAD Geneva University
E-mail: schaad@scsun.unige.ch Department of Biochemistry-SCIENCES-II
Phone: (xx41 22) 702 6478 30, quai E-Ansermet
Fax: (xx41 22) 702 6476 Geneva, Switzerland Ch-1211
-------------------------------------------------------------------
From schaad@scsun.unige.ch Tue Aug 10 05:19:19 1993
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From: Schaad Olivier <schaad@scsun.unige.ch>
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To: charmm-bbs
In-Reply-To: <9308091535.AA18593@emperor.harvard.edu>
Subject: Molecules sitting on axis of symetry
Dear sirs,
I would like to use the IMAGE facility in CHARMM and simulate
with symetry restraint a molecule with a internal symmetry like
Adamantane or benzene 1,5 di pyridine, or hb with water molecules around the
protein
Thank
Olivier Schaad
-------------------------------------------------------------------
Olivier SCHAAD Geneva University
E-mail: schaad@scsun.unige.ch Department of Biochemistry-SCIENCES-II
Phone: (xx41 22) 702 6478 30, quai E-Ansermet
Fax: (xx41 22) 702 6476 Geneva, Switzerland Ch-1211
-------------------------------------------------------------------
From luca@aeolus.ethz.ch Sat Aug 14 08:55:17 1993
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From: Luca Toldo <luca@aeolus.ethz.ch>
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To: charmm-bbs
Subject: CHARMM OPLS for Ammonium Sulphate and Ammonium Acetate ?
Dear Sirs, I wish to know which are the best OPLS parameters to
use for Ammonium Sulphate and for Ammonium Acetate.
Looking forward Your reply
LUCA TOLDO
SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZUERICH
email:Luca@aeolus.ethz.ch
From JARRINM%AM.mrgate@woods.ulowell.edu Sat Aug 14 16:52:53 1993
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Date: Sat, 14 Aug 1993 16:47:13 EDT
From: JARRINM%AM.mrgate@woods.ulowell.edu
To: CHARMM-BBS
X-Vmsmail-To: CHARMM-BBS@EMPEROR.HARVARD.EDU
Message-Id: <0097104B.20420BE0.23273@woods.ulowell.edu>
Subject: Correlation functions
When calculating correlation functions using CHARMm, there are a
few functions to choose from. One of this is called FFT. Can somebody tell me
what is the mathematical fuction FFT stands for?
Also when calculating spectral densities, there are four keywords
to choose from: [SIZE integer] [FOLD] [RAMP] [SWITCH]. What do these keywords
define?
Thank you,
Mario Jarrin
Chemisty Dpt
U. of MA at Lowell
Lowell, MA 01854
e-mail: jarrinm@woods.ulowell.edu
From tennant%hau410.uk.smithkline.com@smithkline.com Fri Aug 20 09:56:10 1993
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Date: Fri, 20 Aug 1993 14:45:04 +0100 (BST)
From: Mike Tennant <tennant%hau410.uk.smithkline.com@smithkline.com>
Subject: Dynamics
To: Charmm Bulletin Board <charmm-bbs%emperor@harvard>
Message-Id: <Pine.3.05.9308201404.W17263-b100000@hau410.uk.smithkline.com>
Mime-Version: 1.0
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Hi all,
Can anybody help with this one...? In a dynamics script, is iasors
0 meant to switch off the use of iasvel and just use iscvel, or does it
use a combination of both? The documentation implies (states) that
just the scaling option will be used, but in practice iasvel seems to be
independant of iasors. Any ideas?
cheers,
Mike.
_____________________________________________________________________________
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Coldharbour Rd |
| | |___ \\|_| | || Harlow |
| \____ \ | _ < || Essex |
| ___| | | |_| | || CM19 5AD |
| \_____/ |____/ || England |
| || Harlow (0279) 622000x3328 |
|_________________________________||__________________________________________|
| |
| Mike Tennant |
| Email: tennant%hau410.uk.smithkline.com@phinet.smithkline.com |
|*****************************************************************************|
| Save the Whales -- Harpoon a Honda. |
-------------------------------------------------------------------------------
From schaad@scsun.unige.ch Fri Aug 27 07:44:20 1993
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Date: Fri, 27 Aug 1993 13:38:37 +0200
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From: Schaad Olivier <schaad@scsun.unige.ch>
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To: charmm-bbs
In-Reply-To: <9308091535.AA18593@emperor.harvard.edu>
Subject: Generate ALL angles and Dihedrals after a PATCH
Dear sirs
Do you known if it is possible to USE the Auto generate Angle and
dihedrals facility after a PATCH.
I would like to Create a new bond between to residues and then generate all
the Angle and Dihedrals and to be sure I am consistent with the
Energy function.
Thank
Olivier Schaad
-------------------------------------------------------------------
Olivier SCHAAD Geneva University
E-mail: schaad@scsun.unige.ch Department of Biochemistry-SCIENCES-II
Phone: (xx41 22) 702 6478 30, quai E-Ansermet
Fax: (xx41 22) 702 6476 Geneva, Switzerland Ch-1211
-------------------------------------------------------------------
From ln@pike.csb.ki.se Fri Aug 27 08:32:06 1993
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To: Schaad Olivier <schaad@scsun.unige.ch>
Cc: charmm-bbs%emperor@harvard
Subject: Re: Generate ALL angles and Dihedrals after a PATCH
In-Reply-To: (Your message of Fri, 27 Aug 93 13:38:37 O.)
<298*/S=schaad/OU=scsun/O=unige/PRMD=switch/ADMD=arcom/C=ch/@MHS>
Date: Fri, 27 Aug 93 14:25:14 +0100
From: "Lennart Nilsson, KI/CSB" <ln@pike.csb.ki.se>
the autogenerate facility does not apply to patches, meaning
that you have to include all relevant angles and dihedrals in the
patch residue definition in the rtf.
lennart nilsson
From brbrooks@helix.nih.gov Fri Aug 27 16:32:51 1993
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Date: Fri, 27 Aug 93 16:27:34 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9308272027.AA19352@helix.nih.gov>
To: charmm-bbs%emperor@harvard, schaad@scsun.unige.ch
Subject: Re: Generate ALL angles and Dihedrals after a PATCH
There is no facility to autogenerate after a patch. This is something
thatt we have wanted for some time, but no one has bothered to write the code.
Bernie Brooks
From silva@yang.mayo.EDU Fri Aug 27 16:44:24 1993
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Date: Fri, 27 Aug 93 15:37:03 -0500
From: silva@yang.mayo.EDU (Norberto Silva)
Message-Id: <9308272037.AA09616@yang.mayo.edu>
To: charmm-bbs
Subject: Stochastic boundary simulations
Hello,
I was wondering if someone would be kind enough to give an example
input file for doing a stochastic boundary simulation. I would also
appreciate if the person donating the input file would also put in a
couple of comments here and there so as to explain why certain
commands or parameter values were chosen in the simulation (I'll
understand though if this is asking for too much). I have already done
a lot of conformational searches with CHARMM as well as a little bit
of dynamics simulation on a whole protein. Thank you.
----------------------------------------------------------------------
Norberto D. Silva, Jr. "Superstition brings bad luck"
Mayo Clinic, Guggenheim 14 --Raymond Smullyan, 5000 B.C.
200 First St. SW
Rochester, MN 55905
FAX: (507) 284-9349
e-mail: silva@mayo.edu phone: (507) 284-5794
----------------------------------------------------------------------
From db3q@engcd.bu.edu Fri Aug 27 17:35:07 1993
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Date: Fri, 27 Aug 93 17:33:38 -0400
From: db3q@engcd.bu.edu (Djamal Bouzida)
Message-Id: <9308272133.AA02136@engcd.bu.edu.bu.edu>
To: CHARMM-bbs
Subject: CHARMM / Monte Carlo
I am writing this message to address the issue of the use of
Monte Carlo methods for studying equilibrium properties of
molecular systems. Many existing packages, including CHARMM,
do not have an option that the user could click to run a
Monte Carlo simulation on the system. Since I've dealt with
the efficiency and the flexibility of such methods during my
PhD thesis, and developed optimized MC methods, I've decided
to find a way on how to connect my routines with the CHARMM
code. The easiest solution I came up with was to link my main
program through the USER routine provided, and then call the
"rebuilding" and "energy-related" routines (SEED,BILDC,GETE,EPROP)
from within my program to rebuild the trial configuration and
update the MC-step. As you may already have guessed, this
procedure is very slow. The reason being that if the trial move
consists of moving only some part of the molecule (say a side
chain), the building routine will have to rebuild the whole
molecule, and the energy routine calculates the new energy of
the whole molecule also. And, since this is repeated many times,
it is very time consuming.
What I need is to rebuild only the new conformation of the
atoms that are moved, and the corresponding energy CHANGE
which is needed for the Metropolis updating process.
Could someone familiar with the routines above please let
me know whether it is possible to do what I described, and
thus increase the efficiency of the code. If yes, please
let me know how. If not, then what COMMON variables are needed
to rebuild only one part of the molecule within CHARMM and
computing the corresponding energy change.
PS: I have another technical request: I believe it should be
possible to call C routines through USER (Calling C from Fortran).
If someone has already done it, I would appreciate receiving a
sample of your code dealing with the interface. ThanQ.
--
Djamal Bouzida E-mail: db3q@engcd.bu.edu
From W.P.vanHoorn@ct.utwente.nl Mon Aug 30 09:27:02 1993
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From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9308301417.AA16177@utctu6.ct.utwente.nl>
Subject: Re: CHARMM / Monte Carlo
To: charmm-bbs (CHARMm BBS)
Date: Mon, 30 Aug 1993 15:16:59 +0000 (WDT)
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Djamal Bouzida writes:
> Many existing packages, including CHARMM,
> do not have an option that the user could click to run a
> Monte Carlo simulation on the system. Since I've dealt with
> the efficiency and the flexibility of such methods during my
> PhD thesis, and developed optimized MC methods, I've decided
> to find a way on how to connect my routines with the CHARMM
> code.
I am very interested in using Monte Carlo within CHARMM. I notice
that 'life-science people' often use Molecular Dynamics, and
'material-science people' use Monte Carlo methods. Is their a
special reason for this? Or am I wrong about this?
(My PhD research consists of a material science subject: self
assembling organic monolayers, and I use the 'life science' program
Quanta/CHARMm, due to historic reasons).
Willem Paul
----------------------------------------------------------------------
(ir) Willem Paul van Hoorn
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (+31)53-892955
P.O. Box 217 (+31)53-892980
7500 AE Enschede, The Netherlands fax : (+31)53-356024
----------------------------------------------------------------------
From kreidler@convex.rz.uni-duesseldorf.de Tue Aug 31 11:51:15 1993
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From: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
Message-Id: <9308311546.AA28723@convex.rz.uni-duesseldorf.de>
Subject: h-bridges in CHARMM 22.0
To: charmm-bbs%emperor@harvard (charmm bbs)
Date: Tue, 31 Aug 1993 17:46:02 +0200 (MET)
Cc: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
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Hi folks out there!
I just read a paper of Milne et al. (J. Mol. Struct. 291, (1993) pp89-103
about "Molecular modeling in solvent". There it is described, that in CHARMM
version 21.2 the calculation of an explicit hydrogen bond term is not possible.
Is this feature implemented in later versions. At the Dept. of Inorganic
chemistry we use Charmm 3.3, which is version 22.0.
Thanx
Kay Kreidler
Dept. of Inorganic chemistry
Heinrich-Heine University Duesseldorf
Germany
From ln@pike.csb.ki.se Tue Sep 7 07:33:47 1993
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To: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
Cc: charmm-bbs%emperor@harvard (charmm bbs)
Subject: Re: h-bridges in CHARMM 22.0
In-Reply-To: (Your message of Tue, 31 Aug 93 17:46:02 O.)
<9308311546.AA28723@convex.rz.uni-duesseldorf.de>
Date: Tue, 07 Sep 93 13:26:39 +0100
From: "Lennart Nilsson, KI/CSB" <ln@pike.csb.ki.se>
the charmm energy function does contain a term for h-bonds; the current
parameterization, however, is made such that this term is not needed with
the coulomb and van der Waals terms taking up also the hbond energy.
a simple distance criterion is usually sufficient to determine if a hydrogen
bond is present or not.
lennart nilsson
END --> aug93.log <---
BEGIN --> sep93.log <---
SEP93.log
--
From ln@pike.csb.ki.se Tue Sep 7 07:33:47 1993
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To: kreidler@convex.rz.uni-duesseldorf.de (Kay Kreidler)
Cc: charmm-bbs%emperor@harvard (charmm bbs)
Subject: Re: h-bridges in CHARMM 22.0
In-Reply-To: (Your message of Tue, 31 Aug 93 17:46:02 O.)
<9308311546.AA28723@convex.rz.uni-duesseldorf.de>
Date: Tue, 07 Sep 93 13:26:39 +0100
From: "Lennart Nilsson, KI/CSB" <ln@pike.csb.ki.se>
the charmm energy function does contain a term for h-bonds; the current
parameterization, however, is made such that this term is not needed with
the coulomb and van der Waals terms taking up also the hbond energy.
a simple distance criterion is usually sufficient to determine if a hydrogen
bond is present or not.
lennart nilsson
From robert@sg1.oc.wau.nl Thu Sep 9 11:34:57 1993
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Date: Thu, 9 Sep 93 17:27:53 +0100
Message-Id: <9309091627.AA28919@Sg1.OC.wau.nl>
To: charmm-bbs
From: Robert Schijvers <robert@sg1.oc.wau.nl>
Subject: ENERGY evaluations
Hi,
When I calculate the minimised energy of a compound using charmm21.3 and
charmm22 I get different
results. All settings and also the PSF's are the same so the parameters
must be changed. In order to
evaluate the energy terms I used: ENERGY IPRINT 1 IMAXP 78 which works well
for charmm21.3 but
is not recognised by charmm22. I could not find an answer for this problem
in the doc files. If anyone
knows an other way to do energy term evaluations please let me know.
Thanks in advance,
Robert.
Robert Schrijvers
Department of Organic Chemistry
Wageningen Agricultural University
The Netherlands
Phone: 31-(0)8370-82364/82368
FAX: 31-(0)8370-84914
E-MAIL: robert@sg1.oc.wau.nl
From brbrooks@helix.nih.gov Thu Sep 9 11:55:50 1993
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Date: Thu, 9 Sep 93 11:50:18 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9309091550.AA09022@helix.nih.gov>
To: charmm-bbs%emperor@harvard, robert@sg1.oc.wau.nl
Subject: Re: ENERGY evaluations
Robert Schrijvers:
The feature which prints out indiviual energy terms was removed
in CHARMM22 and CHARMM23. There is a new analysis facility under development
which will provide this capability, but it will not be available before the end
of the year. For now, you will need to modify the code or write a USERSB or
USERE subroutine to provide this capability (or use an old CHARMM version).
Bernie Brooks
From dchin Thu Sep 9 12:39:10 1993
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From: dchin (Donovan Chin)
Message-Id: <9309091639.AA12754@emperor.harvard.edu>
To: charmm-bbs
Subject: Bernie's response to Robert S.
*From: Donovan Chin
*The charmm-bbs mailer "decided" that Bernie's mail was
*a subscription. It was not and so here it is:
-begin-
Robert Schrijvers:
The feature which prints out indiviual energy terms was removed
in CHARMM22 and CHARMM23. There is a new analysis facility under development
which will provide this capability, but it will not be available before the end
of the year. For now, you will need to modify the code or write a USERSB or
USERE subroutine to provide this capability (or use an old CHARMM version).
Bernie Brooks
From silva@yang.mayo.EDU Thu Sep 9 15:47:02 1993
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Date: Thu, 9 Sep 93 14:39:23 -0500
From: silva@yang.mayo.EDU (Norberto Silva)
Message-Id: <9309091939.AA02248@yang.mayo.edu>
To: charmm-bbs
Subject: equilibration
Hi,
Excuse me for my ignorance in this subject but I tend to get a variety
of advice on the topic of equilibration. I always thought that
a system of N atoms is equilibrated once the temperature T
does not have a percentage fluctuation of more than 1.0/(square root
of N). However, I was later told that one shouldn't look at the
temperature fluctuations but rather the potential energy fluctuations.
Furthermore, I was told that one should equilibrate for as long as
a production run and that rescaling velocities during equilibration
should be less frequent than say the 50 steps (0.001 ps delta time) I
was using for a 1000 atoms simulation. Are there any good references
and/or advice on this topic ? I am in the process of simulating a 100
residue protein in vacuum using CHARMM 22
(with ionizable residue charges reduced by 80%).
----------------------------------------------------------------------
Norberto D. Silva, Jr. "Superstition brings bad luck"
Mayo Clinic, Guggenheim 14 --Raymond Smullyan, 5000 B.C.
200 First St. SW
Rochester, MN 55905
FAX: (507) 284-9349
e-mail: silva@mayo.edu phone: (507) 284-5794
----------------------------------------------------------------------
From db3q@engcd.bu.edu Fri Sep 10 15:29:56 1993
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Date: Fri, 10 Sep 93 15:28:19 -0400
From: db3q@engcd.bu.edu (Djamal Bouzida)
Message-Id: <9309101928.AA13926@engcd.bu.edu.bu.edu>
To: charmm-bbs
Subject: equilibration
silva@yang.mayo.EDU :
> Excuse me for my ignorance in this subject but I tend to get a variety
> of advice on the topic of equilibration. I always thought that
Back to the basics: If you're running MD, the variables that should be
conserved are E (total Energy), N (number of particles), and V (volume)
representing a microcanonical ensemble. Rescaling velocities is done
merely to drive the system to the wanted "equilibrium" state (say at 300K).
At equilibrium, both the kinetic and potential energies will fluctuate
such that the total energy of the system is kept constant. Assuming your
system is large, the mean-square fluctuations of the kinetic energy K
(non-thermodynamic variable) will be <dK^2>/<K> = T[1-3/2C] where C is the
specific heat per particle. If your system is harmonic (and the global
rotation and translation are suppressed in the simulation), the specific heat
per particle is just (3N-6)kB/2N. If you need more details on the subject,
please read the 1967 paper in Physical Review, vol. 153, page 250 titled
"Ensemble Dependence of Fluctuations with Application to Machine Computations."
by Lebowitz, Percus, and L. Verlet. Good luck.
--
Djamal Bouzida E-mail: db3q@engcd.bu.edu
From arne@ewald.mbi.ucla.edu Sat Sep 18 15:04:12 1993
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From: arne@ewald.mbi.ucla.edu (Arne Elofsson)
Message-Id: <9309181857.AA23265@ewald.mbi.ucla.edu>
To: charmm-bbs
Subject: Monte Carlo code for Proteins.
Hi.
Has someone any Monte Carlo code for
proteins. I am looking for full (heavy)
atom based code working in dihedral/angular
space but anything would be welcome.
I'm trying to incorporate some "Monte Carlo"
like features in a genetic algorithm for
all heavy atom proteins.
arne
PS. I now that someone out there has a MC code
for charmm23, but I do not know who and I
do not know how it is implemented.
PPS. Even simplified models, as by Dill, Knapp
etc might be of interest
From chandra@yorvic.york.ac.uk Tue Sep 28 06:26:44 1993
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From: Chandra Verma <chandra@yorvic.york.ac.uk>
Date: Tue, 28 Sep 93 11:17:57 GMT
Message-Id: <15392.9309281117@bill>
To: charmm-bbs%emperor@edu.harvard.harvard
Subject: LIPIDS
Has anyone modelled lipids and lipid/aqueous interfaces. If so i would be
interested in discussing some aspects
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Tue Sep 28 11:52:09 1993
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Date: Tue, 28 Sep 93 11:29:36 EDT
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: lipids
To: CHARMM-BBS
Chandra Verma asked if anyone has modeled lipids and lipid-H2o
interfaces. Tom Woolf, a postdoc with Benoit Roux, has been
working on a small system this past year (WoolfT@ere.umontreal.ca).
He got a set of equilibrated PC structures from Rick Pastor at
the NIH. Rick is associated with Bernie Brooks there. Either Tom
or Bernie can get you Rick's address. My last address for Bernie
was OQI@NIHCU.bitnet.
Also, Berendsen and Van Gunsteren (the Netherlands) reported some
computations: I have references to papers on membranes in
1980, '82, '83, and '86 if you'ld like, and they probably have
other newer stuff.
There was a nice report of a "Molecular Dynamics Simulation
of a Phopholipid Micelle" in a water ball by Wendoloski et al
in Science 243:636-638, 1989.
Hope this helps a little.
-Dave Busath
From heller@nirvana.imo.physik.uni-muenchen.de Tue Sep 28 12:47:27 1993
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Date: Tue, 28 Sep 93 17:39:42 +0100
From: Helmut Heller <Helmut.Heller@physik.uni-muenchen.de>
Message-Id: <9309281639.AA18750@nirvana.imo.physik.uni-muenchen.de>
To: charmm-bbs%emperor@harvard
Subject: lipids
Cc: heller@nirvana.imo.physik.uni-muenchen.de
Hello,
I just wanted to add another recent simulation of a bilayer of 200 POPC
lipds and about 5000 water molecules done by myself, M. Schaefer and
K. Schulten to the list of simulations posted by Dave Busath recently.
The results have been published in the Journal of Physical Chemistry as
@article{HELL92,
author={Helmut Heller and Michael Schaefer and Klaus Schulten},
title={Molecular Dynamics Simulation of a Bilayer of 200~Lipids
in the Gel and in the Liquid Crystal Phases},
journal=JPC,
year=1993,
volume=97,
pages={8343--8360},
note={[Beckman Institute Technical Report UIUC-BI-AI-RCV-92-18 and
UIUC-BI-AI-RCV-93-03]},
loc={Membrane~3}
}
and the pdb files of various structures are available by anonymous ftp
from
ftp@nirvana.imo.physik.uni-muenchen.de
in the directory pub/membrane.
I hope you will find this information helpful,
Helmut Heller
Servus, Helmut (DH0MAD) ______________NeXT-mail accepted_________________
FAX: 089/2805-248 "Knowledge must be gathered and cannot be given"
heller@nirvana.imo.physik.uni-muenchen.de ZEN, one of BLAKES7
Phone: 089/2394-4565 -------------------------------------------------
Helmut Heller, Ludwig Maximilians University
Institute for Medical Optics, Theoretical Biophysics Group
Theresienstr. 37, 80333 Munich, GERMANY
From ryszard@MSI.COM Tue Sep 28 13:04:46 1993
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From: ryszard@MSI.COM (Ryszard Czerminski X 285)
Message-Id: <9309281658.AA15086@hogan.MSI.COM>
To: charmm-bbs
Subject: lipids
During 1993 ACS meeting in Chicago Terry R. Stouch from
Bristol-Myers Squibb (stouch@bms.com) and co-workers
(D. Bassolino, H.E. Alper)
presented results of massive simulations.
Their main interest was in simulating diffusion of
small ligands in biomembranes.
Ryszard Czerminski
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Tue Sep 28 14:38:20 1993
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Date: Tue, 28 Sep 93 14:29:20 EDT
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: lipids
To: CHARMM-BBS
Here is an additional ref plus the refs to the early Groningen work
I alluded to earlier:
EDHOLM, O., AND JOHANSSON, J. 1987. MOLECULAR DYNAMICS STUDIES OF MODEL
MEMBRANES WITH ALFA HELICES. IN STRUCTURE, DYNAMICS, AND FUNCTION OF
BIOMOLECULES. SPRINGER-VERLAG. EHRENBERG, RIGLER, GRASSLUND, & NILSSON,
EDS.
Berendsen and/or van Gunsteren et al. (pre -'87)
Molecular dynamics of model membranes. Biophys. Struct. Mechanisms 6:106
1980. abstract in Supple.
Molecular dynamics of membranes. Thesis by van der Ploeg for Univ. of
Groningen, 1982.
Molecular dynamics of a bilayer membrane. Mol. Phys. 49:233-248. 1983
Conformational entropy of a bilyaer membrane derived from a molecular
dynamics study. Mol. Phys. 48:379-388. 1983.
Molecular dynamics of a bilayer membrane with atomic detail. In:
Structure, Dynamics, and Function of Biomolecules (1986), pp 275-280
Springer.
Hope this helps some more... -Dave Busath
END --> sep93.log <---
BEGIN --> oct93.log <---
OCT93.log
--
Mon, 04 Oct 93 17:31:35 BST
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Date: Sat, 2 Oct 1993 15:27:02 +0100 (BST)
From: Barbara Rosi-Schwartz <spsrosi@reading.ac.uk>
Subject: Vibrational modes analysis
To: CHARMM Bulletin Board <charmm-bbs%edu.harvard.emperor@earn-relay.ac.uk>
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Hello everyone.
Does anybody have a "sample" instruction file for a CHARMm vibratonal
analysis that he/she would be willing to share with me?
I'm trying to explore vibrational dynamics in some polymers, comparing the
CHARMm results with experiment. I've gotten a basic procedure working, but
I must say the analysis of the normal modes obtained is very incomplete;
I would need some advice on a "typical" strategy for it, since the manuals
I've got are not very helpful (using CHARMM from Quanta).
Thanks a lot and do forgive me if I am being a bit naive.
Barbara
/////////////////////
/ /
/////////// /
/ / Barbara Rosi-Schwartz
/ / Polymer Science Centre
/ P O L Y M E R / J.J.Thomson Physical Laboratory
/ / University of Reading, Whiteknights
/ P H Y S I C S / Reading RG6 2AF -- United Kingdom
/ / tel: +44 (0)734 875123 ext. 7605
/ G R O U P / fax: +44 (0)734 750203
/ /////////// e-mail: spsrosi@reading.ac.uk
/ /
///////////
From blandrum@halnet.com Wed Oct 6 09:35:27 1993
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Date: Wed, 6 Oct 1993 08:18:49 -0500
From: blandrum@halnet.com (Bruce E. Landrum)
Message-Id: <9310061318.AA15971@cre1>
To: CHARMM-bbs
Subject: vibrational analysis
Cc:
Barbara Rosi-Schwartz asked about a sample instruction file for a CHARMm
vibrational analysis. Following is a portion of a script that MSI provided to
one of our researchers. It is not well documented, and the CHARMm dictionarydoes not really help all that much.
I've tried to run this with simple molecules, benzene, etc., and have not
gotten very good results. Since the results are only as good as the
information that is fed in, and if you need accurate vibrational analysis,
I feel an ab initio program should be used.
For what its worth, here it is.
===============================================================================
Bruce E. Landrum blandrum@halnet.com
Halliburton Energy Services
P.O. Drawer 1431 Phone 405/251-4470
Duncan, OK 73536-0438 Fax 405/251-4155
===============================================================================
FAST 0
SHAKE OFF
SKIPE NONE
! Do some SD - make sure its minimized
!
MINI SD -
NSTE 1000 NPRI 10 TOLG 0.000000 STEP 0.020000 TOLS 0.000000 TOLENR 0.000100 -
INBFRQ 5 CUTNB 12.000000 CTONNB 8.500000 CTOFNB 9.500000 -
VSHIFT SHIFT CDIE EPS 1.000000 -
IHBFRQ 0 -
IMGFRQ 5 CUTIM 12.5000000
! get energy & print
gete print
printe
iprint
print energy
ic fill
ic purge
!print ic
! Calculate vibrational spectrum
! Vibran requires all energy terms to be defined
vibra
! Diagonalize to generate the normal modes, max atoms = 300
diag
! Potential energy distribution, many options
ped modes 7 thru 24 tole 0.1
!print normal mode information
print norm
STOP
From dchin Wed Oct 6 12:40:35 1993
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Date: Wed, 6 Oct 93 12:40:35 -0400
From: dchin (Donovan Chin)
Message-Id: <9310061640.AA21347@emperor.harvard.edu>
To: charmm-bbs
Subject: A little more on Vibrational analysis
Hello all,
I would like to make a suggestion or two for the vibrational script
that Bruce posted:
In vibrational analysis:
Since you are assuming that only small harmonic modes are occruring
in molecule that is at (or very close) to a energy minimum, you must
first perform a rigorous minimization (after using methods like SD or
CONJ), so use newton raphson, NRAP (i dont think
Stepest Descents is good for vibra analysis, 1st derivatives methods
dont converge well).
If you can not spare the comptational time for NRAP, ABNR is a good compromise.
I would also set the NSTEP value to some high number and set the
tolerance in the energy gradient as the criteria for stopping the minimization
, (tolgrd) on the order of 1e-8 or 1e-12 depending on your level
of error you wish to tolerate (these numbers are my choice).
Remember, if your first 6 modes are not 0 then you are not at
a minimum (charmm spits modes out).
If you have many very low frequencies (0<mode<300cm-1):
I dont know if you are interested in studying a "polymer" chain
(an oligomer realistically) or a monomer, but you should consider`
how much anharmonic modes contribute to rms atomic fluctuations.
If you suspect this, i would look into vibrational methods that
take into account anharmonic contribution, so called "quasi-harmonic
analysis" [Karplus & Kushick "Macromolecules",14,326,(1981) or
Levy, Srinivasan, McCammon, "Biopolymers"23,1099, (1984) are good starts]
A useful piece of charmm script to add to Bruce's script is:
(you can put this after the "print norm" line)
open write unit 22 file name my_modes.dcd
write traj unit 22 mode 7 thru 10 mrms 1.0 -
step 0.02 phase 7.2 ncyc 1
end
stop
Just as you suspect it writes out a charmm dynamics file of certain
modes that you can view in quanta. You can inspect the modes
of motion and plan your next course of action accordingly.
In this case i am writing
modes 7 to 10 and the other commands determine how many frames
for each cycle i want to view. You should find more complete
description of these commands in the online documentation.
There is certaintly more comments that could be added.
regards, Donovan
(UPstairs in the Whitesides group)
-------------------------------------------------------------------
DONOVAN CHIN Harvard University
E-mail: dchin@emperor.harvard.edu Department of Chemistry
Phone: (617) 495-9435 12 Oxford St.
Fax: (617) 495-9857 Cambridge, MA 02138, USA
-------------------------------------------------------------------
From JARRINM%AM.mrgate@woods.uml.edu Wed Oct 6 15:08:28 1993
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Date: Wed, 06 Oct 1993 15:01:19 EDT
From: JARRINM%AM.mrgate@woods.uml.edu
To: CHARMM-BBS
X-Vmsmail-To: CHARMM-BBS@EMPEROR.HARVARD.EDU
Message-Id: <009739E2.1D4BAD40.18515@woods.uml.edu>
Subject: Energy
When doing an energy calculation, is there a way to obtain as part of
the output the energy produced by specific pre-choosen atom interactions? I
need to obtain the individual contribution to the total enrgy of certain
specific atom pairs. Is there a way to do this? I have modified the CHARMm
scripts I have, but with no success so far. If somebody could tell me how
to implement this in a CHARMm script I'll appreciate it. Thank you.
Mario Jarrin
Chemistry Dpt.
U. of MA at Lowell
From MEDCHEM@LIFE.UAMS.EDU Thu Oct 7 01:02:01 1993
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Date: 06 Oct 1993 23:55:33 -0600 (CST)
From: MEDCHEM@LIFE.UAMS.EDU
Subject: MD in acetenotrile
To: charmm-bbs
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We are interested in running a MS simulation in acetenotrile. Does anybody
has try this using charmm?
J. P. Smith
From robert@sg1.oc.wau.nl Thu Oct 7 03:33:17 1993
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From: robert@sg1.oc.wau.nl (Robert Schrijvers)
Message-Id: <9310070727.AA06742@Sg1.OC.wau.nl>
To: charmm-bbs
Subject: RE Energy
A few months ago I asked about the "ENER IPRINT IMAXP" and got the
answer that this did not work in the latest charmm versions. If one
is interested in only specific atom pair interactions the command
"INTEraction [ COMP ] [ NOPRint ] 2x(atom-selection) [UNIT int]" will
calculate the energy terms between the first and second atom-selection.
Robert.
Robert Schrijvers
Molecular Modeling & Design
Department of Organic Chemistry
Agricultural University Wageningen
Dreijenplein 8 6703 HB Wageningen
The Netherlands
Phone: 08370-82364
FAX:08370-84914
e-mail: robert@SG1.OC.WAU.NL
From @ib.rl.ac.uk:spsrosi@reading.ac.uk Tue Oct 12 03:36:42 1993
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Date: Tue, 12 Oct 1993 08:28:10 +0100 (BST)
From: Barbara Rosi-Schwartz <spsrosi@reading.ac.uk>
Subject: vibrational modes analysis -- thanks
To: CHARMM Bulletin Board <charmm-bbs%edu.harvard.emperor@earn-relay.ac.uk>
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I received very enlightening responses to my query on vibrational dynamics
calculations.
Bruce Landrum and Donovan Chin replied publicly, commenting on the
basic VIBRAN commands.
Jeremy Smith, from Saclay, pointed me to a promising JCP paper -- to be
published soon -- in which MD is used to study low frequency
vibrational dynamics in poly(acetylene).
David Perhaia, from Orsay, sent me detailed documentation on
VIBRAN and a very useful (and long!) sample input file.
Finally Krzysztof Kuczera, from Kansas, suggested the use of the alternative
command MOLVIB, again sending a lot of documentation and examples.
A thousand thanks (as we italians say) to all of them, it is indeed an
extremely appreciated (and needed!) contribution.
Anybody who is interested in the details of the replies can feel free to
contact me.
Barbara
/////////////////////
/ /
/////////// /
/ / Barbara Rosi-Schwartz
/ / Polymer Science Centre
/ P O L Y M E R / J.J.Thomson Physical Laboratory
/ / University of Reading, Whiteknights
/ P H Y S I C S / Reading RG6 2AF -- United Kingdom
/ / tel: +44 (0)734 875123 ext. 7605
/ G R O U P / fax: +44 (0)734 750203
/ /////////// e-mail: spsrosi@reading.ac.uk
/ /
///////////
From @ib.rl.ac.uk:spsrosi@reading.ac.uk Tue Oct 12 08:33:56 1993
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Date: Fri, 8 Oct 1993 13:22:39 +0100 (BST)
From: Barbara Rosi-Schwartz <spsrosi@reading.ac.uk>
Original-Sender: Barbara Rosi-Schwartz <spsrosi@reading.ac.uk>
Reply-To: Barbara Rosi-Schwartz <spsrosi@reading.ac.uk>
Subject: Vibrational analysis again
To: CHARMM Bulletin Board <charmm-bbs%edu.harvard.emperor@earn-relay.ac.uk>
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I forgot to mention that anybody who might be interested in the details of
the responses I got can feel free to contact me.
Barbara
/////////////////////
/ /
/////////// /
/ / Barbara Rosi-Schwartz
/ / Polymer Science Centre
/ P O L Y M E R / J.J.Thomson Physical Laboratory
/ / University of Reading, Whiteknights
/ P H Y S I C S / Reading RG6 2AF -- United Kingdom
/ / tel: +44 (0)734 875123 ext. 7605
/ G R O U P / fax: +44 (0)734 750203
/ /////////// e-mail: spsrosi@reading.ac.uk
/ /
///////////
From becky@MSI.COM Tue Oct 12 11:14:24 1993
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From: becky@MSI.COM (Becky Rone X 276)
Message-Id: <9310121508.AA35157@franz.MSI.COM>
To: charmm-bbs
Subject: docking
Does anyone have a copy of the old CHARMM script which docks a small molecule
to a protein? I think it used "lock and key" and the orient commands. Thanks.
From gilquin@goliath.saclay.cea.fr Thu Oct 14 05:14:52 1993
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From: gilquin@goliath.saclay.cea.fr
Message-Id: <9310140910.AA05265@goliath.saclay.cea.fr>
To: charmm-bbs
Hi
People from SGI tall me that a parallelized version of charmm22g2
on SGI machine challenge was develop in Harvard.
I would like to know if this parallelized version of charmm22g2 is available.
Thanks
Sincerely yours
Dr Bernard GILQUIN
Centre d Etude Nucleaire de Saclay
Departement des Sciences du Vivant
Laboratoire d Ingenierie des Proteines
e-mail: gilquin@goliath.sacaly.cea.fr
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From: gilquin@goliath.saclay.cea.fr
Message-Id: <9310140918.AA05308@goliath.saclay.cea.fr>
To: charmm-bbs
Subject: charmm22g2_on_chalange
Hi
People from SGI told me that a parallelized version of charmm22g2
on SGI machine challenge was develop in Harvard.
I would like to know if this parallelized version of charmm22g2 is available.
Thanks
Sincerely yours
Dr Bernard GILQUIN
Centre d Etude Nucleaire de Saclay
Departement des Sciences du Vivant
Laboratoire d Ingenierie des Proteines
e-mail: gilquin@goliath.sacaly.cea.fr
From schaad@scsun.unige.ch Thu Oct 14 08:19:25 1993
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From: Schaad Olivier <schaad@scsun.unige.ch>
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To: charmm-bbs
Subject: CHARMM on IBM SP1
Dear sirs,
I would like to known if somebody has tested CHARMM on the
new parralel computer IBM SP1
Thanks
Olivier Schaad
E-mail schaad@scsun.unige.ch
From brbrooks@helix.nih.gov Wed Oct 20 16:24:38 1993
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Date: Wed, 20 Oct 93 16:18:24 -0400
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <9310202018.AA21497@helix.nih.gov>
To: charmm-bbs%emperor@harvard, schaad@scsun.unige.ch
Subject: Re: CHARMM on IBM SP1
Dear Olivier,
We do have CHARMM running in parallel on the IBM SP1.
Here is a general documentation file concerning the supported
features and appropriate use for parallel CHARMM.
Bernie Brooks
File: parallel, Node: Parallel, Up: (c22doc/charmm.doc), previous: (c22doc/usage.doc), Next: (c22doc/support.doc)
How to use CHARMM on parallel platforms
by Milan Hodoscek and Bernard R. Brooks
CHARMM has been modified to allow computationally intensive simulations
to be run on multi-machines using a replicated data model. This version,
though employing a full communication scheme, uses an efficient
divide-and-conquer algorthm for global sums and broadcasts.
Curently the following hardware platforms are supported:
1. Intel hypercube iPSC/860 gamma machine
2. Intel Delta machine
3. Thinking Machines CM-5
4. IBM SP1 machine
5. Any group of unix machines connected with TCP/IP
===============================================================================
Running CHARMM on parallel systems:
-------------------------------------------------
1. Intel gamma
Because the fortran compiler on the Intel gamma does not know how to rewind the
redirected input file the program uses charmm.inp file name from current
working directory. The script for running CHARMM should look like the
following example:
cp input_file.inp charmm.inp
getcube -t128 > output_file
load ~charmm/c23f2/exec/intel/charmm23
waitcube
Preflx directives required: INTEL UNIX PARALLEL PARAFULL
-------------------------------------------------
2. Intel Delta
mexec "-t(32,16)" ~charmm/c23f2/exec/intel/charmm23 <input_file >output_file &
Preflx directives required: INTEL UNIX DELTA PARALLEL PARAFULL
-------------------------------------------------
3. CM-5
~charmm/c23f2/exec/cm5/charmm23 <input_file >output_file &
Preflx directives required:CM5 UNIX PARALLEL PARAFULL
-------------------------------------------------
4. IBM SP1
I don't know yet.... (CHARMM is fully running, but IBM is still working on OS)
Preflx directives required:IBMRS UNIX IBMSP1 PARALLEL PARAFULL
-------------------------------------------------
5. PARALLEL VERSION OF CHARMM23 ON WORKSTATION CLUSTERS
Preflx directives required: machine_type UNIX PARALLEL SOCKET PARAFULL SYNCHRON
Currently the code runs on HP and IBM RS/6000 machines. This has been
tested. The rest of UNIX world should run too without any changes as
long as the following is true:
-------------------------------------------------
Assumptions for cluster environment:
Before you run CHARMM you have to define some environment variables.
If you define nothing then CHARMM will run in a scalar mode, i.e. default
is one node run. (We could adopt PARALLEL keyword in pref.dat as default.)
PWD
The program supports two shells: KornShell and tcsh, which is
available from anonymous ftp. The only difference on which CHARMM
makes assumption is definition of variable PWD. This variable is
correctly defined in ksh and tcsh by default, so using csh you
sometimes need to define it. Variable PWD points to your current
working directory. If you want that CHARMM uses some other directory
as default you may change it appropriately. The program can figure out
current working directory by itself but there are problems in some NFS
environments, because home directory names can vary on different
machines.( PWD is always defined correctly by shell which supports it! )
So csh may sometimes cause problems. Using csh you may define your cd
command that it always defines also PWD. This is done with something
like:
alias cd 'chdir \!* ; setenv PWD $cwd '
in your ~/.cshrc file.
If you get an error which looks something like nonexistent directory then
define PWD variable directly.
If you want to use tcsh as your login shell you may run the following command:
runall chsh username /usr/local/bin/tcsh
runall is a script which runs the command on the whole cluster of machines
it is on /usr/local/bin at NIH.
NODEx
In order to run CHARMM on more then one node you have to define
environment variables NODE0, NODE1, ... NODEn. Currently then combine
routines support only power of 2 number of nodes, but this will change
in the future.
Example:
4 node run
setenv NODE0 par0
setenv NODE1 par1
setenv NODE2 par2
setenv NODE3 par4
charmm23 < input_file > output_file 1:parameter1 2:parameter2 ...
For this script, "par0,par1,par2,.." is the name of a machine in the local
network. There is no requirement that all machines should be of the same
type. There is nothing in the program to adjust for unequal load balance
so all nodes will follow the slowest one. In near future we may implement
dynamic load balance method based on actual time required.
The assumption here is that the node from where CHARMM program is
started is always NODE0!
Setup for your login environment
In order to run CHARMM in parallel you have to be able to rlogin to
any of the nodes defined in NODEx environment variables. Before you
run CHARMM check this out:
rlogin NODE1
if it doesn't ask you for Password then you are OK. If it asks for
Password then put a line like this:
machine_name user_name
in your ~/.rhosts file.
(This is the same requirement as for running batch system on HP)
How to submit job to HP.
Currently we have assigned machines par0, par1, par2, and par4 to work
in parallel. You may use script /usr/local/bin/charmm23.parallel and
submit it to par0. Example:
submit par0
charmm23.parallel <input_file >output_file
^D
To construct your own parallel scripts look at /usr/local/bin/charmm23.parallel
In the input scripts
Everything should work, but avoid usage of iolev and prnlev in your
parallel scripts.
BUGS: On HPUX when programs execute fork() it copies itself with
double memory requirememnts for a short period of time. This means
that on node zero you have to have enough memory to hold two CHARMM
jobs at once. If this is of any trouble a launcher program may be very
easily written. It will not require much memory and it will be able to
read a file where you can define which node is executing which code,
so this would work also on very complicated network environment.
===============================================================================
Parallel code status (as of October 1993)
The symbol ++ indicates that parallel code development is underway.
------------------------------------------------------
Fully parallel and functional features:
Energy evaluation
ENERgy, GETE
MINImization
DYNAmics (leap frog integrator)
BLOCK
CRYSTAL
IMAGES
CONStraints (SHAKE,HARM,IC,DIHEdral,FIX,NOE)
ANAL (energy partition)
NBONds (generic)
------------------------------------------------------
Functional, but nonparallel code in the parallel version (no speedup):
( ** indicates that these can be very computationally intensive
and are not recommended on parallel systems)
VIBRAN **
CORREL **(Except for the energy time series evaluation, which is parallel)
READ, WRITE, and PRINT (I/O in general)
CORMAN commands
HBONds
HBUIld **
IC (internal coordinate commands)
SCALar commands
CONStraints (setup, DROPlet, SBOUnd)
Miscellaneous commands
GENErate, PATCh, DELEte, JOIN, RENAme, IMPAtch (all PSF modification commands)
MERGE
NBONDS (BYCUbe option)
QUANtum ** ++
QUICk
REWInd (not fully supported on the Intel)
SOLANA
EWALD **
------------------------------------------------------
Nonfunctional code in parallel version:
PERT (just doesn't work yet) ++
ANAL (table generation)
DYNAmics (old integrator, NOSE integrator)
GRAPhics
INTEraction energy
TSM
MMFP
PATH
RISM
TRAVEL
RXNCOR
------------------------------------------------------
Untested Features (we don't know if it works or not):
ANALysis
MOLVIB (No testcase for this code?)
MONItor
NMR
PRESsure (the command)
RMSD
===============================================================================
End.
From xi@garie-beach.rice.edu Wed Oct 20 17:35:00 1993
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Date: Wed, 20 Oct 93 16:28:51 -0500
From: xi@garie-beach.rice.edu (David Xi)
Message-Id: <9310202128.AA14023@garie-beach.rice.edu>
To: charmm-bbs
Subject: lists
Can I get a list of the charmm user?
From tao@ucxray6.berkeley.edu Wed Oct 20 23:01:59 1993
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Date: Wed, 20 Oct 93 19:56:08 -0700
From: tao@ucxray6.berkeley.edu (Tao Zhang)
Message-Id: <9310210256.AA09044@ucxray6.berkeley.edu>
To: charmm-bbs%emperor@harvard
Subject: Get academic charmm
Hi,
I like to know how to get an academic version of Charmm. I am currently
using Charmm22 distributed with Quanta3.3 by MSI (Molecular Simulations
Inc.) Are newer versions of Charmm (> 22) available for academic users ?
Thanks !
T. Zhang
Dept. of MCB
UC Berkeley
From steven@cell.BIH.Harvard.Edu Fri Oct 22 10:02:25 1993
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Date: Fri, 22 Oct 93 09:56:15 EDT
From: steven@cell.BIH.Harvard.Edu (Steven Blechner)
Message-Id: <9310221356.AA00298@cell.bih.harvard.edu>
To: charmm-bbs
I find it necessary to use the "GENERATE SETUP" command on PDB
files that do not have segment name. For small files I have been
using the csh "pdb_charmm" written by T. Mitchell to add a fake
SEGID column to the pdb files. However, when the files are large,
the csh procedure fails (i think it has something to do with a
limit on the total number of characters < 10240...). Before i
write a quick C program:
Does anyone have code to convert large pdb files without segment
names into pdb files WITH segment names added so that CHARMm
can understand them?
-steve
steven@cell.bih.harvard.edu
From steven@cell.BIH.Harvard.Edu Fri Oct 22 10:10:42 1993
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Date: Fri, 22 Oct 93 10:04:32 EDT
From: steven@cell.BIH.Harvard.Edu (Steven Blechner)
Message-Id: <9310221404.AA00323@cell.bih.harvard.edu>
To: charmm-bbs
Subject: pdb to charmm...
I find it necessary to use the "GENERATE SETUP" command on PDB files
that do not have a segment name. For small molecules, I have been
using the csh procedure: "pdb_charmm" written by T. Mitchell to add
a fake SEGID column to the PDB files. However, when the files are
large, the csh procedure fails (i think it has something to do with
a limit on the total number of words < 10240...). Before i write
a quick C program:
Does anyone have code to convert large pdb files without segment
names into pdb files WITH segment names added so that CHARMm can
understand them ?
-steve
steven@cell.bih.harvard.edu
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Fri Oct 22 13:19:10 1993
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Date: Fri, 22 Oct 93 13:05:43 EDT
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: INTE Bug?
To: CHARMM-BBS
In charmm22 (MSI version):
We tried to compute the interaction energy between a calcium ion
and 2799 TIP3 water atoms using:
INTE SELE ATOM CAL * * END SELE ATOM SOLV * * END
After correctly selecting the atoms, charmm dies with a Segmentation
fault. Have we run into a dimension limitation? (The stream file
does nothing else but read in the 2896 atom structure).
-Dave Busath and Rachel Brem
From kmoore@chem.duke.edu Fri Oct 22 16:41:38 1993
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Date: Fri, 22 Oct 93 16:35:13 -0400
From: kmoore@chem.duke.edu (Kevin Moore)
Message-Id: <9310222035.AA26841@dbc2.chem.duke.edu>
To: CHARMM-BBS%emperor@harvard
Subject: mailing list...
Please remove me from the mailing list. Thanks.
{It is probably pointing to kmoore@ncsc.org}
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|| Kevin D. Moore, PhD Tailored Data Solutions, Ltd. ||
|| Programmer/Scientist P.O. Box 37314 ||
|| (804) 275-3946 Richmond, VA 23234 ||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
From arne@ewald.mbi.ucla.edu Sun Oct 24 19:10:52 1993
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From: arne@ewald.mbi.ucla.edu (Arne Elofsson)
Message-Id: <9310242251.AA14417@ewald.mbi.ucla.edu>
To: charmm-bbs
Subject: AMBER/OPLS parameters in CHARMM format.
HI.
As i am in the procedure of testing different
parameters (as well as cutoffs etc) for protein
simulations with charmm, I wonder if someone
has a topology and parameter file with any
other parameter sets than the param 19,20,22.
I would greatly appreciate any other parameter
files.
arne
arne@uclaue.mbi.ucla.edu
From blandrum@halnet.com Mon Oct 25 09:43:20 1993
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Date: Mon, 25 Oct 1993 08:37:21 -0500
From: blandrum@halnet.com (Bruce E. Landrum)
Message-Id: <9310251337.AA27713@cre1>
To: CHARMM-bbs
Subject: CHARMm on SP1
Cc:
One of our researchers has been testing CHARMm on a SP1. This is not
benchmarking, but real research-type testing. His conclusions:
At first the switching technology had a problem, but with the advent of newer
technology, it has improved.
The OS needs great improvement. (As did AIX when it was first released).
Bottom line right now is that you really don't get any improvement in
performance with going to a greater number of nodes. CHARMm running on 4 nodes
does not improve throughput compared to 2 jobs running on 2 nodes. In fact,
it takes longer with 4 nodes. It is questionable whether 2 nodes is better than
1. If you are looking for improvement of wall time, you'll get it. The overhead
is too great at this time for throughput improvement.
Another consideration is that if long-term calculations (some of ours takes
several weeks) are being considered on this (or any) platform, it should not be
done on one which also is being used by a great number of users especially if
they are developing software. The administrator has a tendency to be quick on
the big red (yellow in this case) button.
We are very optimistic about this platform's future. We had one of the first
available 530s. We paid for it with higher prices and less mature OS. We have
decided to wait on this decision until the SP1 is as mature as our current 560.
Thanks,
Bruce E. Landrum
===============================================================================
Halliburton Energy Services blandrum@halnet.com
P.O. Drawer 1431 Phone 405/251-4470
Duncan, OK 73536-0438 Fax 405/251-4155
===============================================================================
From milan@helix.nih.gov Mon Oct 25 10:57:36 1993
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Date: Mon, 25 Oct 93 10:51:00 -0400
From: milan@helix.nih.gov (Milan Hodoscek)
Message-Id: <9310251451.AA05524@helix.nih.gov>
To: blandrum@halnet.com (Bruce E. Landrum)
Cc: CHARMM-bbs%emperor@harvard
Subject: CHARMm on SP1
In-Reply-To: <9310251337.AA27713@cre1>
References: <9310251337.AA27713@cre1>
Bruce E. Landrum writes:
> ______________________________________________________________________
> T H E C H A R M M B B S
>
> One of our researchers has been testing CHARMm on a SP1. This is not
> benchmarking, but real research-type testing. His conclusions:
>
> At first the switching technology had a problem, but with the advent of newer
> technology, it has improved.
>
> The OS needs great improvement. (As did AIX when it was first released).
>
> Bottom line right now is that you really don't get any improvement in
> performance with going to a greater number of nodes. CHARMm running on 4 nodes
> does not improve throughput compared to 2 jobs running on 2 nodes. In fact,
> it takes longer with 4 nodes. It is questionable whether 2 nodes is better than
> 1. If you are looking for improvement of wall time, you'll get it. The overhead
> is too great at this time for throughput improvement.
I don't know how you came to these conclusion but here are our
standard benchmark results for IBM SP1. Unfortunately we have results
only for upto 8 nodes:
Timing in hours for MbCO + 3830 water molecules (14026 atoms), 1000 steps,\\
12-14 \AA\ shift on IBM/SP1.
Nodes & Eext & Eint & Wait$ & Comm & List & Integ& Total & Efficiency & Speedup
1 &21405.6 & 139.6 & 0.0 & 0.1 & 2103.3 & 33.3 &23681.9 = 6.58 h & 100.0 % & 1.0
2 &10835.3 & 77.6 & 243.0 & 83.7 & 1106.5 & 16.7 &12362.7 = 3.43 h & 95.8 % & 1.9
4 & 5358.7 & 47.5 & 214.2 & 130.6 & 609.3 & 9.2 & 6369.4 = 1.77 h & 93.0 % & 3.7
8 & 2622.1 & 30.8 & 275.8 & 165.8 & 354.8 & 5.0 & 3454.2 = 0.96 h & 85.7 % & 6.9
Nodes = How many processors are doing the job.
Eext = nonbonded energy terms
Eint = bonded energy terms
Wait = measure for load unbalance
Comm = Total communication time
List = Update of nonbonded atom list
Integ = time for integration of equations of motions
Total = Total of above in seconds and hours
Efficiency = how much of the machine is lost due to load unbalance and communications
Speedup = speedup over one processor time.
So the bottom line is that it is not so bad machine. The version of
Charmm we are running is a little bit fixed c23f2.
Milan Hodoscek - milan@helix.nih.gov
From blandrum@halnet.com Mon Oct 25 12:13:05 1993
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Date: Mon, 25 Oct 1993 11:07:11 -0500
From: blandrum@halnet.com (Bruce E. Landrum)
Message-Id: <9310251607.AA27266@cre1>
To: CHARMM-bbs
Subject: CHARMm on SP1
Cc:
It has been pointed out by both Milan Hodoscek and my cohort that I was more
negative than I meant to be and did not represent myself correctly. I
apologize to one and all.
Some clarifications (I hope):
There is always going to be some overhead associated with running on a
parallel platform. It all depends upon how much of the overall job is
parallelized and how much time is spent in communications between nodes.
In the results sent by Milan Hodoscek, it shows that at 8 nodes it costs 1
machine to run that job (ca 16%). To us, that is an acceptable overhead.
Some of the routines in CHARMm have not been parallelized. When SHAKE was, it
actually cost time, so it was not parallelized. My cohort used periodic
boundaries, which currently is not parallelized, on a system of similar size.
In his calculations (which I don't have the numbers, only his account-the
report is coming), it costs slightly over 1 machine at 4 nodes. So he says
that it is better to have 2 jobs running on 2 nodes (only about 10% overhead)
than 1 job running on 4 nodes with > 25% overhead. Also, because of not being
parallelized, the job with short cutoffs had a greater overhead than that with
long cutoffs, that is it spent more time in the non-parallelized/
communications portion.
My cohort also says that with the earlier ethernet switching technology, that
communications was a bottleneck, but that this has been taken care of.
I hope that this clears up my interpretation.
Thanks,
Bruce E. Landrum
===============================================================================
Halliburton Energy Services blandrum@halnet.com
P.O. Drawer 1431 Phone 405/251-4470
Duncan, OK 73536-0438 Fax 405/251-4155
===============================================================================
From milan@helix.nih.gov Mon Oct 25 15:54:28 1993
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Date: Mon, 25 Oct 93 15:47:25 -0400
From: milan@helix.nih.gov (Milan Hodoscek)
Message-Id: <9310251947.AA27568@helix.nih.gov>
To: blandrum@halnet.com (Bruce E. Landrum)
Cc: CHARMM-bbs%emperor@harvard
Subject: CHARMm on SP1
In-Reply-To: <9310251607.AA27266@cre1>
References: <9310251607.AA27266@cre1>
Bruce E. Landrum writes:
>
> Some clarifications (I hope):
>
> Some of the routines in CHARMm have not been parallelized. When SHAKE was, it
> actually cost time, so it was not parallelized. My cohort used periodic
> boundaries, which currently is not parallelized, on a system of similar size.
Both SHAKE (within groups) and periodic boundaries works fine in
parallel version. A week ago Bernie Brooks send parallel.doc file to
this BBS where everything what works and what does not in parallel
version of CHARMM was explained in more details.
Milan Hodoscek (milan@helix.nih.gov)
From wahle@mace.cc.purdue.edu Tue Oct 26 11:35:39 1993
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Date: Tue, 26 Oct 93 10:29:24 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9310261529.AA23777@mace.cc.purdue.edu>
To: charmm-bbs
Subject: Energy calculations
Dear all,
I am having a problem trying to understand an energy calculation that I am
using from someone else's script file. I have asked that individual and
he is unaware of what is happening. I have also looked in the CHARMm
manuals and have found only limited help. The script is below:
Energy -
INBF 50 ALL CUTHB 0.5 CUTHBA 90.0 ACCE -
HBNO CTONHB 0.0 CTOFHB 0.0 CTONHA 50.0 CTOFHA 70.0 -
INBF 50 ELEC ATOM NOEX NOGR NOQU CDIE SWIT -
VDW VATOM VSWI VDIS -
ST2L -
CUTNB 8.0 CTONNB 6.5 CTOFNB 7.5 CTEXNB 999.0 -
SIGCUT 1.5 SIGADD 0.5 SIGON 1.25 SIGOFF 1.5 -
WMIN 1.5 WRNMXD 0.5 SIGMAX 7.5 SIGWRN 0.7 -
EPS 1.0 NORXN EPSEXT 80.0 ORDER 10 SHELL 2.0 E14F 1.0
What do the commands that begin with SIG mean? NOEX? NOGR? NOQU? VDIS? ST2L?
NORXN? EPSEXT? ORDER? SHELL? Are these commands from an earlier version of
CHARMm? Looking in the .log file, none of these commands produce an error.
Other questions arise there. What are the nonbond option flags BYGRoup,
NOEXtnd, and NOEWald? The log file also shows KAPPA values, KMAX, KSQMAX,
NBXMOD, and CTEXNB. What do these variables represent? As I have said,
I consulted the CHARMm dictionary manuals and have found no evidence of
these variables/commands under the nonbonding specs. I know that the first
two lines for the energy calculation are hydrogen bonding specs and I understand
them, but the other parts I have indicated are confusing.
The whole purpose of this is that I am minimizing a structure after the
energy is calculated and I want to make sure that the energy calculation and
the minimization calculation are using the same variable limits. Any help
that can be given will be greatly appreciated.
Mark C. Wahle
Dept. of Medicinal Chemistry
Purdue University
e-mail: wahle@mace.cc.purdue.edu
END --> oct93.log <---
BEGIN --> nov93.log <---
NOV93.LOG
----------
From wahle@mace.cc.purdue.edu Tue Nov 2 09:45:51 1993
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Date: Tue, 2 Nov 93 09:39:36 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9311021439.AA04494@mace.cc.purdue.edu>
To: charmm-bbs
Subject: CHARMm energy calc
Dear Everyone:
I am having a problem trying to understand an energy calculation that I am
using from someone else's script file. I have asked that individual and
he is unaware of what is happening. I have also looked in the CHARMm
manuals and have found only limited help. The script is below:
Energy -
INBF 50 ALL CUTHB 0.5 CUTHBA 90.0 ACCE -
HBNO CTONHB 0.0 CTOFHB 0.0 CTONHA 50.0 CTOFHA 70.0 -
INBF 50 ELEC ATOM NOEX NOGR NOQU CDIE SWIT -
VDW VATOM VSWI VDIS -
ST2L -
CUTNB 8.0 CTONNB 6.5 CTOFNB 7.5 CTEXNB 999.0 -
SIGCUT 1.5 SIGADD 0.5 SIGON 1.25 SIGOFF 1.5 -
WMIN 1.5 WRNMXD 0.5 SIGMAX 7.5 SIGWRN 0.7 -
EPS 1.0 NORXN EPSEXT 80.0 ORDER 10 SHELL 2.0 E14F 1.0
What do the commands that begin with SIG mean? NOEX? NOGR? NOQU? VDIS? ST2L?
NORXN? EPSEXT? ORDER? SHELL? Are these commands from an earlier version of
CHARMm? Looking in the .log file, none of these commands produce an error.
Other questions arise there. What are the nonbond option flags BYGRoup,
NOEXtnd, and NOEWald? The log file also shows KAPPA values, KMAX, KSQMAX,
NBXMOD, and CTEXNB. What do these variables represent? As I have said,
I consulted the CHARMm dictionary manuals and have found no evidence of
these variables/commands under the nonbonding specs. I know that the first
two lines for the energy calculation are hydrogen bonding specs and I understand
them, but the other parts I have indicated are confusing.
The whole purpose of this is that I am minimizing a structure after the
energy is calculated and I want to make sure that the energy calculation and
the minimization calculation are using the same variable limits. Any help
that can be given will be greatly appreciated.
Mark C. Wahle
Dept. of Medicinal Chemistry
Purdue University
e-mail: wahle@mace.cc.purdue.edu
PS: I sent this message over a week ago but have not received a reply. Does
anyone have any idea about what's going on above?
From KUN12@caos.caos.kun.nl Tue Nov 2 11:16:27 1993
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Date: Tue, 2 Nov 1993 17:07:57 METDST
From: KUN12@caos.caos.kun.nl
Subject: CHARMm energy calculations
To: charmm-bbs%emperor@harvard
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Hi Marc,
I have simular problems with the CHARMm manuals: the most important
things are missing!!
About the commands: I don't know all the answers to your questions,
but some.
The nonbonded spec NOEX means no extended electrostatics used; NOGR
means no gradient; NOQU means no quadripoles taken into account,etc.
You can find some hints about how these things work in the document-
files. I don't know anything about the SIG-commands or ST2 etc.
I guess that NOEW means that no Ewald summations are used in the
electrostatics.
My question is about Ewald summations: Does anyone know how this
works in CHARMm22.0?? I tried, but I can't find anything about it
neither in the manual, nor in the documentfiles.
best regards,
Reinier Grimbergen.
--------------------------------------------------------------------------------
RIM labatory of Solid State Chemistry / / \ \ / / / \ / /
University of Nijmegen / / / / / / / /\ / /
Toernooiveld / / \ \ / / / / / /
tel: 080-653071 / / / / / / / / / /
e-mail:kun12@caos.caos.kun.nl / / / / / / / / / /
--------------------------------------------------------------------------------
From bobf@MSI.COM Tue Nov 2 15:15:54 1993
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Message-Id: <9311022009.AA10124@lurch>
From: Bob Funchess <bobf@MSI.COM>
Date: Tue, 2 Nov 1993 15:09:30 -0500
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
To: quanta-l@MSI.COM
Subject: energy keywords
Cc: charmm-bbs
In general, a description of the various keywords can be found in one of
the files in the $CHM_DATA/doc directory. For the specific keywords that Mark
mentions, most of them are given in $CHM_DATA/doc/nbonds.doc; there are a
couple of exceptions (KMAX is from cons.doc and NBXMode is from struct.doc).
As Craig just mentioned, the documentation issue has been discussed here in
the past. MSI is aware of the problem; the support group will be going
through the CHARMm dictionary to clear up "Appendix A" and to document the
keywords of which no mention at all is made in the printed manuals (like the
ones in Mark's script).
Regards,
Bob Funchess
--
Dr. Robert B. Funchess Molecular Simulations Inc.
Scientific Support 16 New England Executive Park
bobf@msi.com Burlington, MA 01803-5297
(617) 229-9800 x202 FAX (617) 229-9899
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Tue Nov 2 16:51:04 1993
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Date: Tue, 02 Nov 93 16:31:32 EST
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: SGI installation problem
To: CHARMM-BBS
I am trying to compile charmm22g2 (July 7, 1992) to correct a small
error in rxndef.src that prevents DISTance definition for umbrella
sampling, but I am having trouble with cstuff.c compilation. Two
questions: 1) Is there an updated version of rxncor that I should
be using instead of the version I have? 2) Why might I get this
error message:
accom: Error: /usr/people/busath/charmm/source/machdep/cstuff.c, line 110:
One declaration for getpwuid is non-prototype style, with one prototype;
prototype must match default argument promotions (ANSI 3.5.4.3, 3.3.2.2)
struct passwd *getpwuid(); *getpwptr;
?
I have used both 4.0.1 and 4.0.5 versions of the SGI operating system.
Xiaoling Liang at Harvard thought I must have a bad /usr/include/pwd.h
because she had no trouble compiling cstuff.c on her sgi. She sent me
her /usr/include/pwd.h and I recompiled with it, but got the same error
message. (I could verify easily that her version of pwd.h was being
used). Unfortunately, she is at a seminar now; does anybody else
recognize this problem?
Thanks in advance,
David Busath
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Tue Nov 2 19:04:23 1993
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Date: Tue, 02 Nov 93 18:53:46 EST
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: SGI compile
To: CHARMM-BBS
Thanks to Kim Andrews at Rice and Leo at Harvard for the suggestion
that I add the -cckr switch to the cc command in machdep.mk. According
to Leo, this is an SGI c compiler switch that allows one to stray from
ANSI standards. It worked for cstuff.c compilation. -Dave Busath
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Tue Nov 2 22:29:49 1993
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Date: Tue, 02 Nov 93 22:14:51 EST
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: compilation woes
To: CHARMM-BBS, Mike Pear <MPEAR@MSI.COM>, Xiaoling Liang <lia@tammy>,
Benoit Roux <ROUXB@ERE.UMontreal.CA>,
Bernie Brooks <OQI%NIHCU.BITNET@BROWNVM.brown.edu>
Trying to compile last years charmm22 (g2) with this year's SGI
operating system (4.0.5), I'm running into two roadblocks. If
anyone is awake and can give me a clue tonight, I'd be grateful...
1) nbonds.f refuses to compile because, in line 1114 (part of a
reasonably short if statement): "out of tree space; simplify expression"
2) space.f refuses to compile because, on line 164 (B+MALLOC(CODE)),
: "attempt to use an untyped function"
Perhaps space.f needs to be compiled with a c preprocessor? nbonds.f,
I have no clue. -Dave
From wahle@mace.cc.purdue.edu Wed Nov 3 15:43:57 1993
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Date: Wed, 3 Nov 93 15:37:41 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9311032037.AA17771@mace.cc.purdue.edu>
To: charmm-bbs
Subject: CHARMm energy update
To all who replied:
Thanks for all your help. The online documentation has provided a lot of
answers. Unfortunately I am a relative novice with CHARMm (6 months) and
up to this time have only been able to learn about the parts of CHARMm I
use with each project. We grad students don't have much to go into much
depth on a lot of things. I have inquired about CHARMm short courses
offered by MSI, and hopefully I'll have the time to take them next spring
or summer. Until then, I hope I won't bore this bulletin board with too
many stupid questions. (Since when was a question ever stupid?)
Special thanks to Randy Zauhar, Chandra Verma (very much so), Reinier
Grimbergen, Bruce Bush, Tom Hendrickson, Roland Stote, Bob Funchess (MSI
wizard!), and Mike Tennant! Both the MSI bulletin board and CHARMm
bulletin board gave helpful advice. As for the inadequacies with the
documentation, which was a hot topic here a few months back, I agree 100%.
A novice like myself needs to have more information available, and the
screen copies in the text are nice but don't explain anything more than
what I can already see on the screen in front of me! It would save me
and I'm sure many others a lot of time if the manuals were able to answer
more of our questions. Bob Funchess, or anyone else at MSI who might read
this, PLEASE make the improvements in the new documentation worthwhile!!
Until next time...
Mark C. Wahle
Dept. of Medicinal Chemistry
Purdue University
email: wahle@mace.cc.purdue.edu
A famous Roman philosopher once wrote, "SEMPER UBI SUB UBI!!!!"
From @UKCC.UKY.EDU:CSC001@UKCC.UKY.EDU Mon Nov 8 12:51:34 1993
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Date: Mon, 08 Nov 93 12:34:27 EST
From: CSC001@UKCC.uky.edu
Subject: minimizing solvated peptide
To: charmm-bbs
I have found fluctuations in energy during minimization of a 'cyclic'
peptide (diameter approx 15A) in a 30A box, following essentially the
same script as for "solvated glycerol: 7.1-18 polygen charmm manual).
The delta-E values can be +200 then -200 kcal/mol in successive steps,
followed by termination because "function tol. 0.0 satisfied". The
minimization always stops right after a nonbonded list update.
Similar results are obtained with:
UPDAtes 50, 20, 10 or 5 (though more stable with lower values)
cutnb 15 or 8
SD or ABNR with variety of step sizes (0.02 to 0.00001)
with or without shake bonh
Frequently, the geometry of the solute is deformed by the minimization,
leading to problems with equilibration.
Any advice would be appreciated.
David Ward
University of Kentucky
From @BROWNVM.BROWN.EDU:BUSATH@BROWNVM.BROWN.EDU Tue Nov 9 14:30:39 1993
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Date: Tue, 09 Nov 93 14:19:24 EST
From: David Busath <BUSATH@BROWNVM.brown.edu>
Subject: umbrella
To: CHARMM-BBS
Has anyone out there used rxnc, the new umbrella sampling subroutine,
to define a linear reaction coordinate (e.g. the ratio of two distances)?
We are having some startup problems that seem to be due to errors
in the distance definitions. We're using charmm22,g2.
-Dave Busath
From nicolas@david.saclay.cea.fr Fri Nov 12 04:00:16 1993
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Date: 12 Nov 93 09:49:22+0100
From: "30MO SBPM Nicolas FOLOPPE" <nicolas@david.saclay.cea.fr>
Message-Id: <9311120849.AA04688@david.saclay.cea.fr>
To: charmm-bbs
Subject : how to calculate the energy of part of a system
with CHARMM ?
I am facing the following basic problem : how to
compute with CHARMM the potential energy of only part of a whole
protein ? Let's call REAC that part of the protein
for which I need the energy. That energy is the sum of
the self energy of REAC (bonded + nonbonded
terms) plus the interaction energy between REAC
and rest of the protein (bonded and nonbonded terms).
I calculated that energy using either the "INTE" subcommand
or the "CONS FIX" subcommand.
Using INTE (inte sele REAC end sele all end), I've got
that result :
---------- --------- --------- --------- --------- ---------
INTE> 1 -901.69311 .00000 1.74967
INTE INTERN> 39.15927 88.98846 3.38105 94.72567 11.82383
INTE EXTERN> -391.35521 -748.41618 .00000 .00000
---------- --------- --------- --------- --------- ---------
Using CONS FIX (cons fix sele all .and. .not. REAC ),
I obtain another result :
---------- --------- --------- --------- --------- ---------
ENER> 0 -864.08161 .00000 5.66944
ENER INTERN> 39.15927 95.87168 3.38105 123.84037 13.43740
ENER EXTERN> -391.35521 -748.41618 .00000 .00000
---------- --------- --------- --------- --------- ---------
What surprise me is that some terms (bonds,Urey-Bradley,elec,vdw)
are equal although some are not (impropers, dihedrals,valence
angles).
Is there something wrong in the way I handle those commands ?
Is there a rational behind those differences ?
Any help or advice is welcomed,
Nicolas Foloppe
From nicolas@david.saclay.cea.fr Mon Nov 15 06:03:01 1993
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Date: 15 Nov 93 11:51:54+0100
From: "30MO SBPM Nicolas FOLOPPE" <nicolas@david.saclay.cea.fr>
Message-Id: <9311151051.AA17719@david.saclay.cea.fr>
Subject: How to calculate energy locally ?
To: charmm-bbs
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Length: 1743
Subject : how to calculate the energy of part of a system
with CHARMM ?
I am facing the following basic problem : how to
compute with CHARMM the potential energy of only part of a whole
protein ? Let's call REAC that part of the protein
for which I need the energy. That energy is the sum of
the self energy of REAC (bonded + nonbonded
terms) plus the interaction energy between REAC
and rest of the protein (bonded and nonbonded terms).
I calculated that energy using either the "INTE" subcommand
or the "CONS FIX" subcommand.
Using INTE (inte sele REAC end sele all end), I've got
that result :
---------- --------- --------- --------- --------- ---------
INTE> 1 -901.69311 .00000 1.74967
INTE INTERN> 39.15927 88.98846 3.38105 94.72567 11.82383
INTE EXTERN> -391.35521 -748.41618 .00000 .00000
---------- --------- --------- --------- --------- ---------
Using CONS FIX (cons fix sele all .and. .not. REAC ),
I obtain another result :
---------- --------- --------- --------- --------- ---------
ENER> 0 -864.08161 .00000 5.66944
ENER INTERN> 39.15927 95.87168 3.38105 123.84037 13.43740
ENER EXTERN> -391.35521 -748.41618 .00000 .00000
---------- --------- --------- --------- --------- ---------
What surprise me is that some terms (bonds,Urey-Bradley,elec,vdw)
are equal although some are not (impropers, dihedrals,valence
angles).
Is there something wrong in the way I handle those commands ?
Is there a rational behind those differences ?
Any help or advice is welcomed,
Nicolas Foloppe
END --> nov93.log <---
BEGIN --> dec93.log <---
DEC93.log
--
From wahle@mace.cc.purdue.edu Wed Dec 8 16:51:20 1993
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Date: Wed, 8 Dec 93 16:44:31 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9312082144.AA26872@mace.cc.purdue.edu>
To: charmm-bbs
Subject: CHARMm image specs
Dear all,
Can anyone explain more clearly what IXTFRQ is and what it does under the
image-specs? I've looked in the on-line help (images.doc) as well as some
other of those documentation files, but the explanation their is too vague.
All I'm doing is setting up a ABNR minimization with images and am trying to
write a script to do so, but I'm not too clear on IXTFRQ. Thanks for the
help in advance.
Mark C. Wahle
Department of Medicinal Chemistry
Purdue University
email: wahle@mace.cc.purdue.edu
From wahle@mace.cc.purdue.edu Sun Dec 12 16:37:06 1993
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Date: Sun, 12 Dec 93 16:30:16 -0500
From: wahle@mace.cc.purdue.edu (mark wahle)
Message-Id: <9312122130.AA06227@mace.cc.purdue.edu>
To: charmm-bbs
Dear all,
These are the three responses I received regarding my earlier question
concerning IXTFRQ for CHARMm image specs. I hope that these three notes
will shed some light on this topic for others as much as it has for me.
Thanks to all those who supplied this info.
Mark C. Wahle
Department of Medicinal Chemistry
Purdue University
*****
MESSAGE NUMBER ONE:
*****
From ryszard@msi.com
Dear Mark,
IXTFrq is a frequency of updating crystal structure.
It is relevant only if you are using CRYSTAL facility.
If you are e.g. dealing with a flexible polymer
it is important to update crystal to take into account
conformational changes of the polymer, if it is
changing e.g. from coil to extended chain.
If you are dealing with well defined crystal composed
of small molecules, and you know that no big
scale changes will occur you may set it up to something
big (e.g. 1000).
Ryszard
*****
AND MESSAGE NUMBER TWO:
*****
Dear Mark,
IXTFRQ is used for updating list of crystal transformations
i.e. list of unit cells which will be created
IMGFRQ is used for updating image atom list
i.e. list of atoms WITHIN image unit cells
For example crystal which initially looks like
I I I I I
I I P I I
I I I I I
may look in following way after crystal update
(governed by IXTFRQ)
I I I
I I I
I P I
I I I
I I I
Again this is functional only if you are using crystal
facility and is not if you are using only
nearest neighbours (and/or directly images).
Ryszard
P.S. I will notify our documentation department about
missing IXTFRQ information. Thank you for pointing
it out.
*****
AND MESSAGE NUMBER THREE:
*****
From: David Ward <CSC001@UKCC.uky.edu>
I saw your message on the CHARMM bbs
i have had some problems doing solvated peptide calculations using CHARMm
from MSI. There is a problem with the image centering facility. The short
answer is leave out image centering and then minimization appears to work
ok. I have problems with molecular dynamics though.
Here's a script for you to modify and try. The solute has segment ID 1s.
Try it with and without commenting out image centering (commented out
in this script).
The ixtfrq is the frequency of image updates if the primary box was
built using the crystal facility (i think).
If you get any good information on all this, or see any errors in
what i've said please let me know.
! Startup script for CHARMm
!
UPPER ! CASE FOR FILES TO WRITE
OPEN WRITE CARD UNIT 7 NAME CHARMM.LOG
banner
bomblevel -2
wrnlev 0
prnlev 5
OPEN READ CARD UNIT 21 NAME /MASSES.RTF.H
read rtf card unit 21
close unit 21
OPEN READ CARD UNIT 21 NAME /AMINOH.RTF.H
read rtf card unit 21 append
close unit 21
OPEN READ FILE UNIT 21 NAME /PARM.BIN.H
read param file unit 21
close unit 21
! This script generates the psf
!
DELE ATOM SELECT ALL END
read sequ quanta
* Read sequence using special QUANTA option
*
14
CYS 1 CYS 2 GLU 3 LEU 4 CYS 5 CYS 6
ASN 7 PRO 8 ALA 9 CYS 10 THR 11 GLY 12
CYS 13 TYR 14
GENERATE 1S SETUP
OPEN READ UNIT 18 CARD NAME STHGC4.CRD
READ COOR UNIT 18 CARD
COOR ORIE
READ SEQU TIP3 1000
GENE SOLV SETU NOANGLE
OPEN READ UNIT 14 CARD NAME /BOX30.CRD.H
READ COOR UNIT 14 CARD APPE
DELE ATOM SELE ( .BYRES. ( SEGID SOLV .AND. TYPE OH2 .AND. -
( ( .NOT. SEGID SOLV .AND. .NOT. HYDROGEN ) -
.AROUND. 2.80 ) ) ) END
SET 9 31.1032
OPEN READ UNIT 15 CARD NAME /WATERBOX.IMG.H
READ IMAG UNIT 15 CARD
CLOSE UNIT 15
! below, image centering commented out
! IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE SEGI SOLV END
SHAKE OFF
SKIPE NONE
UPDA CUTNB 8.0 CUTIM 8.0 INBFRQ 1 IHBFRQ 0 IMGFRQ 1 - ! PUT IN HERE
CTONNB 6.5 CTOFNB 7.5 WMIN 1.5 ! BECAUSE OF
! CUTIM ERROR
NBONDS VSWITCH SHIFT NBXMOD 5
ENER
! PRIN IMAGE FORCES PSF
COOR COPY COMP
CONS FIX SELE SEGI 1S END
UPDA INBFRQ 20 IMGFRQ 20 IHBFRQ 0
MINI SD NSTEP 20 STEP 0.02 NPRINT 10
MINI ABNR NSTEP 1000 TOLGRD 0.0001 STEP 0.001
CONS FIX SELE NONE END
UPDA INBFRQ 20 IMGFRQ 20 IHBFRQ 0
MINI ABNR NSTE 10000 STEP 0.0001 TOLGRD 0.00001 TOLENR 0.0000000 -
NPRINT 100
COOR RMS MASS
COOR RMS MASS SELE SEGID 1S END
COOR RMS MASS SELE SEGID SOLV END
COOR RMS MASS SELE ATOM SOLV * OH2 END
IC FILL
IC DIFF
! PRINT IC
! WRITE MINIMIZED COORDINATES TO DISK
OPEN WRIT UNIT 88 CARD NAME DG_M_5M5.CRD.B
WRIT COOR UNIT 88 CARD
* SOLVATED MINIMIZED COORDINATES
*
OPEN READ UNIT 15 CARD NAME /CLEARBOX.IMG.H
READ IMAG UNIT 15 CARD
CLOSE UNIT 15
STOP
From dchin Mon Dec 13 12:21:21 1993
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id AA06188; Mon, 13 Dec 93 12:21:21 -0500
Date: Mon, 13 Dec 93 12:21:21 -0500
From: dchin (Donovan Chin)
Message-Id: <9312131721.AA06188@emperor.harvard.edu>
To: charmm-bbs
Subject: Re: IXTFrq
(reposted by Donovan Chin)
This is a response to an earlier question posted about IXTFrq:
:::
Orig. Question:
:::
Can anyone explain more clearly what IXTFRQ is and what it does under the
image-specs? I've looked in the on-line help (images.doc) as well as some
other of those documentation files, but the explanation their is too vague.
All I'm doing is setting up a ABNR minimization with images and am trying to
write a script to do so, but I'm not too clear on IXTFRQ. Thanks for the
help in advance.
Mark C. Wahle
:::
response
:::
Dear Mark,
IXTFrq is a frequency of updating crystal structure.
It is relevant only if you are using CRYSTAL facility.
If you are e.g. dealing with a flexible polymer
it is important to update crystal to take into account
conformational changes of the polymer, if it is
changing e.g. from coil to extended chain.
If you are dealing with well defined crystal composed
of small molecules, and you know that no big
scale changes will occur you may set it up to something
big (e.g. 1000).
IXTFRQ is used for updating list of crystal transformations
i.e. list of unit cells which will be created
IMGFRQ is used for updating image atom list
i.e. list of atoms WITHIN image unit cells
For example crystal which initially looks like
I I I I I
I I P I I
I I I I I
may look in following way after crystal update
(governed by IXTFRQ)
I I I
I I I
I P I
I I I
I I I
Again this is functional only if you are using crystal
facility and is not if you are using only
nearest neighbours (and/or directly images).
Ryszard
P.S. I will notify our documentation department about
missing IXTFRQ information. Thank you for pointing
it out.
-------------------------------------------------------------------
DONOVAN CHIN Harvard University
E-mail: dchin@emperor.harvard.edu Department of Chemistry
Phone: (617) 495-9435 12 Oxford St.
Fax: (617) 495-9857 Cambridge, MA 02138, USA
-------------------------------------------------------------------
From silva@yang.mayo.EDU Mon Dec 13 15:03:50 1993
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Date: Mon, 13 Dec 93 13:56:51 -0600
From: silva@yang.mayo.EDU (Norberto Silva)
Message-Id: <9312131956.AA13087@yang.mayo.edu>
To: charmm-bbs
Subject: charmm 22 installation question
Hi,
We recently got the CHARMM 22 installation package and we have one
question about it. I know this will sound more like a unix
question but believe me we looked into the man pages and we cannot
understand why the -m option was used in the very last command line of the
makefile listed below. What does it do and why is it needed. I tried
contacting (via e-mail) the current CHARMM 22 maintanence person about this
but he/she has yet to respond. Thank you.
# CHARMM 22 makefile for SGI IRIS machines
ROOT = rootdir
SRC = $(ROOT)/source
FLX = $(ROOT)/tool/preflx
LIB = $(ROOT)/lib/sgi
EXEC = $(ROOT)/exec/sgi
FC = f77 -col120 -Ns1000 -Nn8000 -Nx300
CC = cc
LD = f77
.SUFFIXES: .fcm .src .o
VPATH = fcm
FC0 = $(FC) -c -O0 -static
FC1 = $(FC) -c -O1
FC2 = $(FC) -c -O2
FC3 = $(FC) -c -O3
FCR = $(FC) -c -O2
FCD = $(FC) -c -no -g
FCRD = $(FC) -c -re -no -g
LIBS = \
$(LIB)/correl.a \
$(LIB)/dynamc.a \
$(LIB)/energy.a \
$(LIB)/gener.a \
$(LIB)/graphics.a \
$(LIB)/io.a \
$(LIB)/machdep.a \
$(LIB)/main.a \
$(LIB)/manip.a \
$(LIB)/minmiz.a \
$(LIB)/misc.a \
$(LIB)/molvib.a \
$(LIB)/nbonds.a \
$(LIB)/image.a \
$(LIB)/energy.a \
$(LIB)/pert.a \
$(LIB)/quantum.a \
$(LIB)/rxncor.a \
$(LIB)/util.a \
$(LIB)/vibran.a
$(EXEC)/charmm22 : $(LIB)/charmm.o $(LIBS)
$(LD) -o charmm22.exe $(LIB)/charmm.o -m $(LIBS)
#
----------------------------------------------------------------------
Norberto D. Silva, Jr. /\ /\
Mayo Clinic, Guggenheim 14 / \__/ \
200 First St. SW (@@)
Rochester, MN 55905 \/
FAX: (507) 284-9349
e-mail: silva@mayo.edu phone: (507) 284-5794
----------------------------------------------------------------------
From eldbjorg@chem.uit.no Wed Dec 15 15:51:16 1993
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Date: Wed, 15 Dec 93 21:45:04 -0800
From: eldbjorg@chem.uit.no
Message-Id: <9312160545.AA03736@trypsin.chem.uit.no>
To: charmm-bbs
Subject: H-bonds
I am interested in analysing hydrogen bonds
as a function of time during molecular dynamics
simulations (use of .DCD files) and would really
appreciate information about how other CHARMm users
do this.
Thanks in advance,
Elle
#######################################################
# Eldbjoerg Sofie Heimstad #
# Protein Crystallography Group #
# University Of Tromsoe, IMR #
# 9037 Tromsoe, NORWAY phone: +47-83-45706 #
# 44737 #
# fax : +47-83-44765 #
# E-mail: eldbjorg@trypsin.chem.uit.no #
#######################################################
From brbrooks@helix.nih.gov Thu Dec 16 15:02:37 1993
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Date: Thu, 16 Dec 1993 14:53:14 -0500
From: brbrooks@helix.nih.gov (Bernie Brooks)
Message-Id: <199312161953.OAA23011@helix.nih.gov>
To: charmm-bbs%emperor@harvard, eldbjorg@chem.uit.no
Subject: Re: H-bonds
Dear Elle:
The CORREL section of CHARMM has a hydrogen bond section to it.
It allows the evaluation of particular Hbonds as a function of time.
The drawback to the code is that you must first provide a list of
potential hbonds that you would like to consider. This can be done
by merging (and deleting duplications) a series of hbond card files
generated from simulation frames.
Bernie Brooks
From becky@MSI.COM Thu Dec 16 15:42:08 1993
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Date: Thu, 16 Dec 1993 15:31:19 -0500
From: becky@MSI.COM (Becky Rone X 276)
Message-Id: <9312162031.AA17800@franz.MSI.COM>
To: brbrooks@helix.nih.gov, charmm-bbs%emperor@harvard, eldbjorg@chem.uit.no
Subject: Re: H-bonds
If the system is not too complicated you can use QUANTA; Dynamics Animation
(redraw Hbonds) to see the hydrogen bonds as they flicker in and out and from
this generate the initial list of hydrogens which participate in Hbonding.
However, if you are accomplished at CHARMM commands and the use of editors
you might be better to generate the list based on the simulation frames.
In either case, CORREL still needs to be used.
From dhuhta@MSI.COM Thu Dec 16 16:48:32 1993
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Date: Thu, 16 Dec 1993 16:36:08 -0500 (EST)
From: Dave Huhta <@MSI.COM:dhuhta@gomez>
Subject: Re: H-bonds
To: Becky Rone X 276 <becky@MSI.COM>
Cc: brbrooks@helix.nih.gov, charmm-bbs%emperor@harvard, eldbjorg@chem.uit.no
In-Reply-To: <9312162031.AA17800@franz.MSI.COM>
Message-Id: <Pine.3.07.9312161606.C5085-a100000@gomez>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
On Thu, 16 Dec 1993, Becky Rone X 276 wrote:
>
> If the system is not too complicated you can use QUANTA; Dynamics Animation
> (redraw Hbonds) to see the hydrogen bonds as they flicker in and out and from
> this generate the initial list of hydrogens which participate in Hbonding.
> However, if you are accomplished at CHARMM commands and the use of editors
> you might be better to generate the list based on the simulation frames.
> In either case, CORREL still needs to be used.
If you do the dynamics animation as described, Quanta will create a file
(fort.45) with a list of the hydrogen bonds (with distances and angles, etc.)
on a frame by frame basis.
Dave.
dhuhta@msi.com
From wphoorn@utctu2.ct.utwente.nl Fri Dec 17 06:28:26 1993
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From: wphoorn@utctu2.ct.utwente.nl (Willem Paul van Hoorn)
Message-Id: <9312171121.AA16544@utctu2>
Subject: Urey-Bradley energy
To: charmm-bbs (CHARMm BBS)
Date: Fri, 17 Dec 1993 12:21:08 +0100 (MET)
X-Mailer: ELM [version 2.4 PL5]
Content-Type: text
Content-Length: 988
Hi CHARMM users,
I noticed that in charmm22 there is also a Urey-Bradley enery term.
I found a article by Rossky, Karplus and Rahman (Biopolymers 1979)
in which a 1-3 correction term is described as follows:
Eangle = K(theta - theta0)^2 + F(L-L0)^2 + 2F'(L-L0)
theta is the B-A-C angle and L is the B---C distance:
A
/ \
B---C
However, in the parameter list there is only one equilibrium distance
(L0?) and one force constant. Is this force constant F or F' or are
they the same?
Thanks for helping me,
Willem Paul
----------------------------------------------------------------------
(ir) Willem Paul van Hoorn
University of Twente e-mail: wphoorn@ct.utwente.nl
Organic Chemistry Department phone : (+31)53-892955
P.O. Box 217 (+31)53-892980
7500 AE Enschede, The Netherlands fax : (+31)53-356024
----------------------------------------------------------------------
From mitchell_t%frgen.dnet@sb.com Fri Dec 17 12:26:37 1993
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Date: Fri, 17 Dec 93 11:58:00 -0500
Message-Id: <9312171658.AA05983@phinet.smithkline.com>
From: mitchell_t%frgen.dnet@sb.com
To: charmm_bbs@phinet.smithkline.com
Subject: Harmonic constraints query
Hi everyone,
I'm having a problem setting harmonic constraints on a protein/ligand
complex. I'm using SCALAR CONS RECALL .. to set the costraints on the
protein, prior to a Langevin Dynamics run, and CONS HARM SELE ....
to set contraints on two atoms of the ligand.
The Dynamics falls over straight away with energy change exceeded. In
the energy breakdown, the CONS energy and hence the potential energies
are sky high (i.e. ********), which is presumably screwing up the
dynamics.
If I do a PRINT CONS to list the constraints, I get two columns of atoms
and a forece constant for each. In nearly all cases, the two atoms are
the same, as one might expect. But, in some of the protein atoms, and
for the ligand, the first and second atoms are NOT the same; the first
atom seems to be constrained to it's "neighbour" -- hence a high
constraint energy => screwy dynamics.
My questions are:
Am I doing something daft ? (it is Friday afternoon, after all)
Has anyone come across this before ? Do you have a workround ?
Is this a known bug. ?
I'm using CHARMm22 from MSI on 4 processors of a SG380s
Thanks in advance of any help. Have a good X-mas or whatever you are
celbrating.
Tim Mitchell
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone: (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax: (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || E-Mail: mitchell_t%frgen.dnet@sb.com U.K. |
-------------------------------------------------------------------------------
From alex@tammy Fri Dec 17 13:27:59 1993
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Date: Fri, 17 Dec 93 13:22:04 -0500
From: alex@tammy (Alex Mackerell)
Message-Id: <9312171822.AA10551@tammy.harvard.edu>
To: charmm-bbs, wphoorn@utctu2.ct.utwente.nl
Subject: Re: Urey-Bradley energy
CHARMM only uses the quadratic term (F(L-L0)^2) for the
Urey-Bradley term.
Alex MacKerell
From dchin Fri Dec 17 14:32:00 1993
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id AA12109; Fri, 17 Dec 93 14:32:00 -0500
Date: Fri, 17 Dec 93 14:32:00 -0500
From: dchin (Donovan Chin)
Message-Id: <9312171932.AA12109@emperor.harvard.edu>
To: charmm-bbs
Subject: Urey-Bradley energy
--
Since charmm-bbs thinks that messages that contain < 100 characters
are "possible subscriptions," (i.e. prevents things like "subscribe..
unsubscribe.." from getting distributed over charmm-bbs), it sends these
to me and not the list.
Therefore, I am re-posting Alex's response to Willem's question
about Urey-Bradley energy (if short messages occur often, I will disable this
feature).
Regards, Donovan (bbs-manager)
--
orig question:
Eangle = K(theta - theta0)^2 + F(L-L0)^2 + 2F'(L-L0)
theta is the B-A-C angle and L is the B---C distance:
A
/ \
B---C
However, in the parameter list there is only one equilibrium distance
(L0?) and one force constant. Is this force constant F or F' or are
they the same?
response:
CHARMM only uses the quadratic term (F(L-L0)^2) for the
Urey-Bradley term.
Alex MacKerell
-------------------------------------------------------------------
DONOVAN CHIN Harvard University
E-mail: dchin@emperor.harvard.edu Department of Chemistry
Phone: (617) 495-9435 12 Oxford St.
Fax: (617) 495-9857 Cambridge, MA 02138, USA
-------------------------------------------------------------------
From mitchell_t%frgen.dnet@sb.com Tue Dec 21 11:12:53 1993
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Date: Tue, 21 Dec 93 10:57:59 -0500
Message-Id: <9312211558.AA29849@phinet.smithkline.com>
From: mitchell_t%frgen.dnet@sb.com
To: charmm_bbs@phinet.smithkline.com
Subject: Harmonic Constraints II
Thanks to Bernie Brooks and Leo Caves for the solution to my problem
with harmonic constraints. Doing a
CONS HARM SELE ATOM * * * END FORCE 0.00000001 before the SCALAR CONS...
commands means that the dynamics seems to run OK (It hasn't fallen over
after 2ps now!). However, the PRINT CONS listing still indicates that
some atoms aren't constrained to themselves. Is this a problem with
PRINT CONS ?. Can someone at Harvard/MSI check it out ?
Have a good holiday .. .. .. Tim Mitchell
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone: (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax: (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || E-Mail: mitchell_t%frgen.dnet@sb.com U.K. |
-------------------------------------------------------------------------------
From mitchell_t%frgen.dnet@sb.com Thu Dec 23 07:47:20 1993
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Date: Thu, 23 Dec 93 07:26:59 -0500
Message-Id: <9312231227.AA07457@phinet.smithkline.com>
From: mitchell_t%frgen.dnet@sb.com
To: charmm_bbs@phinet.smithkline.com
Subject: Sbounds -- how do you turn it off ?
Hi -- I'm docking a series of ligands into a protein active site and
doing a minimise-dynamics-minimise procedure. I'm using one CHARMm
script to dock in all the ligands, and doing a DELE ATOM SELE ALL END
to clear everything out before reading in the protein and new ligand.
A solvent boundary is set up using SBOUND before the Langevin Dynamics
My problem is that the "first" ligand docks OK, but the second one
gets into trouble during the initial minimisation. Basically is has a
huge SBOUND energy (~-80000 Kcal), but no solvent boundary should be set
up for this protein/ligand complex at this stage. It appears that the
DELE ATOM SELE ALL has not removed the solvent boundary constraints from
the previous simulation.
Is this a bug?
Is there any way I can turn off the solvent boundary "manually"?
Thanks in advance for any help -- have a good X-mas break.
Tim.
-------------------------------------------------------------------------------
| _____ ____ || SmithKline Beecham Pharmaceuticals Ltd |
| / ___\\\\ _ \ || Brockham Park |
| | |___ \\|_| | || Tim Mitchell (Comp. Chem.) Betchworth |
| \____ \ | _ < || Phone: (0)737 36 4535 Surrey |
| ____| | | |_| | || Fax: (0)737 36 4539 RH3 7AJ |
| \_____/ |____/ || E-Mail: mitchell_t%frgen.dnet@sb.com U.K. |
-------------------------------------------------------------------------------
From allelix@utcc.utoronto.ca Wed Dec 29 11:12:55 1993
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id AA04858; Wed, 29 Dec 93 11:12:55 -0500
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From: <allelix@utcc.utoronto.ca>
To: charmm-bbs
Message-Id: <93Dec29.110544est.18663@gpu.utcc.utoronto.ca>
Date: Wed, 29 Dec 1993 11:05:34 -0500
Greetings Charmm users,
I am in the process of looking for ways to test some models of
protein receptors I have generated by homology modelling and wish to
sample your opinions on the value of interaction energies as a measure
of a ligand's binding affinity. In the case where one ligand has a binding
affinity which is a factor of ten different for two receptors I anticipate
a different interaction energy (nonbonded interactions) which should
correlate with the binding affinity. I get some success but have a few
anomolous results which may be due to the imperfections in my models.
I am curious if there is any experience in this area out there and
if so I would appreciate hearing from you. I would be interested in your
opinions on interaction energies and on the optimal way to evaluate
a protein receptor model's validity.
Thank-you
Robert Kirby
Comp. Chemist/Molecular Modeller
Allelix Biopharmaceuticals Inc.
Allelix Biopharmaceuticals Inc.
Mississauga Ont., Canada.
allelix@utcc.utoronto.ca
From allelix@utcc.utoronto.ca Wed Dec 29 11:40:41 1993
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Received: by gpu.utcc.utoronto.ca id <18663>; Wed, 29 Dec 1993 11:33:31 -0500
From: <allelix@utcc.utoronto.ca>
To: charmm-bbs
Subject: Interaction Energies
Message-Id: <93Dec29.113331est.18663@gpu.utcc.utoronto.ca>
Date: Wed, 29 Dec 1993 11:33:25 -0500
Greetings Charmm Users,
I am trying to evaluate the validity of some protein receptors
I have generated by homology modelling and wish to correlate the
non-bonded interactions between some ligands and my proteins with
binding affinities. I get anomolous results in some cases and have not
found reference to this in the literature. I therefore wish to sample
your opinions on how to best test protein models and if you have tried
interaction energies with known ligands.
In principal I believe correlation should be possible in cases
where one ligand has differential binding to a couple of proteins since
desolvation energies can be eliminated (ie same ligand two proteins).
Any wisdom or experience in this area would be appreciated.
Thank-you
Robert Kirby
Comp. Chem/Mol. Modeller
Allelix Biopharm.
Mississauga Ont., Canada.
allelix@utcc.utoronto.ca
END --> dec93.log <---