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Date: Mon, 22 Apr 2002 07:16:46 +0200
To: Yunfeng Hu <yunfeng@chem.ucla.edu>
From: Per-Ola Norrby <pon@kemi.dtu.dk>
Subject: Re: CCL:programs to extract md needed force constants from g98
 calculation
Cc: chemistry@ccl.net
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	Hi,

>I'm trying to write a force parameter file for a inhibitor with sulfite
>substituents. Since the major force fields do not have them, I use g98 to
>generate the force constants. I wonder if there are any softwares that
>can change g98 output into the md format force constants. Thanks!

	Not completely straightforward, has to be done in a way that 
is compatible with the existing parts of the force field.  Have a 
look at:

"Automated Molecular Mechanics Parameterization with Simultaneous 
Utilization of Experimental and Quantum Chemical Data"
Per-Ola Norrby and Tommy Liljefors, J. Comput. Chem. 1998, 19, 1146-1166

"Deriving Force Field Parameters for Coordination Complexes"
Per-Ola Norrby and Peter Brandt, Coord. Chem. Rev. 2001, 212, 79-109

"Recipe for an organometallic force field"
Per-Ola Norrby, in Computational Organometallic Chemistry, Ed: T. 
Cundari; Marcel Dekker: New York, 2001, 7-37

	There are also numerous citations in these (in particular in 
the CCR review), to work dealing with general force field 
parameterization, by Hagler, Halgren, Rasmussen, Allinger, Dillen, ...

	Regards,

	Per-Ola
-- 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/
Technical University of Denmark, Dept. of Chem., Org. Chem.
Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
Email: pon@kemi.dtu.dk  tel +45-45252123,  fax +45-45933968

From chemistry-request@server.ccl.net Mon Apr 22 04:45:04 2002
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Date: Mon, 22 Apr 2002 10:46:33 +0200
From: Giuseppe Ermondi <giuseppe.ermondi@unito.it>
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Hi CCL,

first of all I would like to thank CCL and the person who wrote me very
interesting
answers to my question.

I apologize with Jerome because I did not forward him the messages but I
hope that
this summary was usefull!

Thank to David, I think that the references that you
suggested me is sufficiente for my proposal.

Thanks to Sergio, I think that the reference that you named was:

Automatic parameterization of force field by systematic search and
genetic algorithms
Wang JM, Kollman PA
JOURNAL OF COMPUTATIONAL CHEMISTRY
22 (12): 1219-1228 SEP 2001

Finally thank to Vlad who suggested me a good web site with usefull
information.

Now the summary!

Best  regards,

Giuseppe

============================================================
Original question:
-----------------

Hi CCL,

I am working with Autodock and GROMACS and I am looking for
articles, reviews or other material regarding two subjects:

1) how can evaluate charge distribution for molecules or groups like
heme
in order to obtain reasonable charges (coherent with "classical" sets
like
Amber or Kollman charges)? Are there any compilations of charges for
uncommon
groups?

2) how can obtain reasonable parametrization for the same groups? Are
there
databases available for the more usefull programs?

Thank you

Regards

Giuseppe Ermondi

================================================================
================================================================
Jerome wrote:
--------------
Hi Giuseppe

I would appreciate if you could forward me answers you get on your
question.
CHARMM parameters and topology for for Ferrous (Fe2+) heme  can be found
at
the following URL:

http://www.pharmacy.umaryland.edu/faculty/amackere/research.html


look at:

par_all27_prot_lipid.inp
top_all27_prot_lipid.inp

I am looking for parameters for Ferric (Fe3+) heme for use with CHARMM.
If
you ever have information about that, I'd be glad to know...

Ciao,
Jerome


----------------------------------------------------------
Jerome Baudry, Ph.D.
Computational Research Scientist,
Research Coordinator
150 Noyes Lab.

Computer Applications & Network Services
School of Chemical Sciences
University of Illinois at Urbana-Champaign
505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801

Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3210; E-mail:
jerome@scs.uiuc.edu
============================================================
David wrote:
-------------

Giuseppe,

For groups like heme, and other common cofactors, it is most likely that

complete parameters exist - I know that heme is part of the standard
CHARMM protein parameter sets, and I expect that AMBER parameters exist
for it as well.  I'm not sure where to look for these, but if you look
around on the AMBER site: http://www.amber.ucsf.edu/amber/, you should
be able to find some direction.  For less common molecules, and
virtually
all drugs, you'll most likely have to come up with your own charges -
and
possibly other parameters.

Associated with the AMBER package is a program RESP - which I believe
can
be obtained separately and for free - which fits partial atomic charges
to an electrostatic potential obtained from QM calculations.  This is, I

believe, the method of choice for obtaining new charges for use in
AMBER.
I've appended BibTex entries for the two papers describing RESP, and a
few links you might like to check out are
http://www.amber.ucsf.edu/amber/charges.txt
, which is a describing of the charge fitting philosophy of the Kollman
group written by Wendy Cornell, and
http://www.amber.ucsf.edu/amber/Questions/resp.html
, which has some FAQs about RESP. Of course there are many other methods

for obtaining charges, some based of fitting the QM ESP, others based on

empirical methods, but I focussed on RESP here since you seem to be
using
the Kollman group force fields.  If you want more info about some of the

other methods, just let me know and I'd be glad to send you a bigger
list
of references.

@Article{resp1,
  author =       {Bayly, C. I. and Cieplak, P. and Cornell, W. D. and
Kollman, P. A.},
  title =        {A well-behaved electrostatic potential based method
using
charge restraints for determining atom-centered charges:  The {RESP}
model},
  journal =      jpc,
  year =         1993,
  volume =       97,
  pages =        {10269-10280},
  group =        {Kollman}
}

@Article{resp2,
  author =       {Cornell, W. D. and Cieplak, P. and Bayly, C. I. and
Kollman, P. A.},
  title =        {Application of {RESP} charges to calculate
conformational
energies, hydrogen bond energies, and free energies of solvation},
  journal =      jacs,
  year =         1993,
  volume =       115,
  pages =        {9620},
  group =        {Kollman}
}

Hope this helps!

David

--
-------------------------------------------
David F. Green
Department of Chemistry
Massachusetts Institute of Technology
77 Massachusetts Ave., Rm. 6-133
Cambridge, MA 01239
Phone: 617-258-6229
Fax:   617-253-7030
Email: dfgreen@lms.mit.edu
-------------------------------------------
======================================================
Vlad wrote:
------------

Take a look at the AMBER data base on the web...As far as I remember
there are parameters there for heme.
vlad

=======================================================
Sergio wrote,
-------------

Dear Giuseppe,

    The best way to obtain relaible charges is to use ESP charges (MK or

CHELPG) calculated by  quantum mechanical method (HF/6-31G(d) for
example).
For AMBER force field the best is to calculate charges by RESP method.n
There some programs to parametrize stretchings,  bendings and torsional
terms in a force field. I use PAPQMD developed by F.J. Luque, M. Orozco
and
C. Aleman, in Barcelona (http://www.bq.ub.es/recmol/soft.html), but in
J.
Comp. Chem., , 2001 there is a paper from Kollman that presents a new
method
for parameterization (sorry I don't find it ).

        Hope this help,

                    Sergio


    ==============================================================
Sergio Emanuel Galembeck
Assistant Professor in Physical Chemistry
Laboratorio de Modelagem Molecular
Departamento de Quimica
Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto
Universidade de Sao Paulo
Av Bandeirantes, 3900
Ribeirao Preto, SP
Brasil

phone: +55-16-602-37-65
fax: +55-16-633-81-51
e-mail: segalemb@usp.br
==============================================================


_____________________________________________________________________
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From chemistry-request@server.ccl.net Mon Apr 22 05:32:36 2002
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From: Szilveszter Juhos <szilva@ribotargets.com>
To: song yunlong <songyunlong@hotmail.com>
cc: chemistry@ccl.net
Subject: Re: CCL:solutions about how to execute the InsightII software from
 a PC desktop
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On Sun, 21 Apr 2002, song yunlong wrote:
> Can you kindly provide me some solutions about how to execute the
> InsightII software from a PC desktop.

Hello, if you browse through the CCL archive you will be able to find a
quite long discussion about it. Apparently it is not solved yet, you have
to have an SGI or on a remote X display run 

insightII -nosplash -opengl  #never worked for me

or 

insightII -nosplash -axxess  #not that good quality

Szilva


From chemistry-request@server.ccl.net Mon Apr 22 08:28:50 2002
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Date: Mon, 22 Apr 2002 08:28:34 -0400
From: Praveen M Bahadduri <bahadduri.1@osu.edu>
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Hi! CCL,

I am working with autodock for some time. I had a recurring problem. I am
reposting this question.

When I run autodock program and read the docked pdb file in sybyl window, I get
a bunch of straight lines with dots. I cannot figure out if there is any
specific arrangement of these lines or dot. I carried it several times, but in
vain.

Can anybody please let me know solution to this problem?

Sincerely

Praveen

The Ohio-State University
Columbus, OH.


From chemistry-request@server.ccl.net Mon Apr 22 10:49:41 2002
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  CCLers:
  I am trying some problems that use lots of memory and disk space.
In particular an ROVGF calculation on cytosine to determine the IP.
My computer runs out of disk space when writing the integrals to an
.rwf file.  Some friends have said to split this file into segments
using %rwf=a,1989mb,b,1989mb,c,1989mb, etc.
  This actually works for a few more minutes. i.e. the problems
continues execution but eventually crashes.  Looking at the scratch
files I note that a.rwf is pretty big, and b.rwf is gigantic.  But
nothing is written in c.rwf, etc.  So I presume I have again run out
of disk space?  But this time I have no warning, just a core dump 
and a failed execution.
  Any hints on what to try next?
  Regards, Dave Close. 



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From chemistry-request@server.ccl.net Mon Apr 22 22:19:12 2002
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	Tue, 23 Apr 2002 02:18:56 +0000
From: dkeidel397@att.net
To: chemistry@ccl.net
Subject: convergence failure
Date: Tue, 23 Apr 2002 02:18:56 +0000
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Hello all,

I am new to the gaussian98 (and Gaussian in general) so I
hope that this question is not remedial.  I am running my
first calculation and I recieve the following error:

 >>>>>>>>>> Convergence criterion not met.
 SCF Done:  E(RHF) =  -2466.88014462     A.U. after   65
cycles
             Convg  =    0.1379D-03             -V/T = 
2.0051
             S**2   =   0.0000
 KE= 2.454261151979D+03 PE=-8.251028945559D+03 EE=
2.134018806627D+03
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /usr/local/g98/l502.exe.


I tried to add the line:  Opt=(MaxCycle=30) since someone
here told me to try that, but I do not think that will
solve my problem.  I would greatly appreciate any help in
this manner.  Thank you in advance and have a great day.
 I have pasted my input file below.

#P HF/STO-3G pop=(chelpg, readrad) density=current
Opt=MaxCycle=400

HF/STO-3G//HF/STO-3G 


0 1
  C    1 r2 
  C    2 r3    1 a3
  C    3 r4    2 a4    1 d4
  C    4 r5    3 a5    2 d5
  C    1 r6    2 a6    3 d6
  C    4 r7    3 a7    2 d7
  C    7 r8    4 a8    3 d8
  C    8 r9    7 a9    4 d9
  C    5 r10    4 a10    3 d10
  C    9 r11    8 a11    7 d11
  O    11 r12    9 a12    8 d12
  O    11 r13    9 a13    8 d13
  C    2 r14    1 a14    3 d14
  O    14 r15    2 a15    1 d15
  O    14 r16    2 a16    1 d16
  Zn    12 r17    11 a17    9 d17
  H    1 r18    2 a18    3 d18
  H    3 r19    2 a19    1 d19
  H    6 r20    1 a20    2 d20
  H    7 r21    4 a21    3 d21
  H    8 r22    7 a22    4 d22
  H    10 r23    5 a23    4 d23
Variables:
r2= 1.4192
r3= 1.3871
a3= 119.97
r4= 1.4055
a4= 120.68
d4=   0.03
r5= 1.4353
a5= 119.38
d5= 359.96
r6= 1.3713
a6= 120.80
d6= 359.97
r7= 1.4294
a7= 121.89
d7= 179.97
r8= 1.3639
a8= 121.33
d8= 179.97
r9= 1.4318
a9= 119.91
d9= 359.97
r10= 1.3982
a10= 119.60
d10= 180.03
r11= 1.4173
a11= 119.91
d11= 179.97
r12= 1.3318
a12= 125.08
d12=   0.03
r13= 1.3328
a13= 124.98
d13= 179.97
r14= 1.5382
a14= 119.45
d14= 180.03
r15= 1.2565
a15= 116.60
d15= 180.66
r16= 1.2569
a16= 116.42
d16=   0.71
r17= 2.0197
a17=  92.37
d17= 179.88
r18= 1.1058
a18= 116.95
d18= 179.97
r19= 1.1037
a19= 118.39
d19= 179.92
r20= 1.0995
a20= 121.18
d20= 179.97
r21= 1.1028
a21= 117.89
d21= 359.88
r22= 1.1009
a22= 121.65
d22= 179.97
r23= 1.1040
a23= 119.82
d23= 180.03

Thanks,

Don

--
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and 
Molecular Biology
Riverside, CA 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dkeidel397@att.net


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Subject: Comp Chem Courses ... complete undergrad program!
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Hello everybody ...
=20
Sorry for this late reply but I just got back from the Structure-Based
Drug Design conference in Boston ... Over there, I met two teachers from
University of New Brunswick (that's right ... in Canada!) that offer
what seems to be a complete undergraduate program in computational
chemistry. This program consists of both chemistry and "computer"
courses and the program is now on the 2nd year of the first group (as I
understand it). What makes it interesting is that the computational
chemistry course has been set up in interactive FLASH, and the students
have access to all the files in order to make their learning easier. I
haven't really checked out their web page but maybe you can find
something at www.unb.ca ... good luck!
=20
Axel Mathieu, Ph.D.
Computational Chemist
NEOKIMIA INC.
www.neokimia.com <http://www.neokimia.com/>=20
=20
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<TITLE>Message</TITLE>

<META content=3D"MSHTML 5.00.3315.2870" name=3DGENERATOR></HEAD>
<BODY>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D897204020-22042002>Hello =
everybody=20
...</SPAN></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><SPAN=20
class=3D897204020-22042002></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><SPAN class=3D897204020-22042002>Sorry =
for this late=20
reply but I just got back from the Structure-Based Drug Design =
conference=20
in&nbsp;Boston ... Over there, I met two teachers from University of New =

Brunswick (that's right ... in Canada!) that offer what seems to be a =
complete=20
undergraduate program in computational chemistry. This program consists =
of both=20
chemistry and "computer" courses and the program is now on the 2nd year =
of the=20
first group (as I understand it). What makes it interesting is that the=20
computational chemistry course has been set up in interactive FLASH, and =
the=20
students have access to all the files in order to make their learning =
easier. I=20
haven't really checked out their web page but maybe you can find =
something at <A=20
href=3D"http://www.unb.ca">www.unb.ca</A> ... good =
luck!</SPAN></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV align=3Dleft><FONT face=3DArial size=3D2>Axel Mathieu, =
Ph.D.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Computational Chemist</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>NEOKIMIA INC.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><A=20
href=3D"http://www.neokimia.com/">www.neokimia.com</A></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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From chemistry-request@server.ccl.net Mon Apr 22 18:57:56 2002
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Date: Mon, 22 Apr 2002 15:59:04 -0700
From: "PR@AeonTechnology.com" <pr@AeonTechnology.com>
Subject: Release of Direct Force Field, Version 1.1.3
To: chemistry@ccl.net
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Aeon Technology Inc. is pleased to announce the general availability of
Direct Force FieldT 1.1.3.
Direct Force FieldT is not just another force field. It is an expert system
that can be used to automatically create force field parameters from ab
initio data.

A patent-pending process that helps fit very complex potential energy
surfaces efficiently has been implemented in Direct Force FieldT. This
technique enables fast and reliable development of force field parameters
> from ab initio data. In addition, this product can be used to generate
approximated parameters without fitting data or to convert parameters from
one force field to another.

The result parameters can be used independently or cooperatively with
existing force fields by popular simulation engines such as AMBER, CHARMM
and DISCOVER.

Please visit www.AeonTechnology.com for more information on our company and
on the product.





