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From: Tackley Daniel R - INTE <Daniel.Tackley=at=intertekasg.com>
To: "Comp Chem Mailing List (E-mail)" <CHEMISTRY=at=server.ccl.net>
Subject: Molekel and G03
Date: Fri, 28 May 2004 14:31:45 +0100
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Hi All,

I have been using Molekel in conjunction with G98 for the last couple of
years and have been very happy with the quality of analysis that I have been
able to achieve with this combination.

The upgrade from G98 to G03 has led to a few problems, most of which arise
> from the slightly updated layout of the new G03 output file. The main
problems seem to come from the geometry section since on opening the output
file, the molecule in Molekel comes out flattened into 2-dimensions. I can
still manage most visualisations by using cube files but the one analysis
that is not possible is that of vibrational modes. This data can only be
obtained from the G03 output file.

I've tried contacting CSCS (Swiss National Supercomputing Centre) who hold
the rights but their (automated) respone was that they aren't providing any
support. Attempts to get hold of the source code to try to correct it myself
also failed.

Does anyone have any suggestions on:

1. Has anyone else solved this problem?

2. How I might get access to the source code for Molekel?

3. Any other programs that I could use to visualise vibrational modes
(animations and vectors if possible)


Thanks for your help,

Daniel Tackley

--
Dr Daniel Tackley
Computational Chemistry Group
Intertek ASG
PO Box 42
Hexagon House
Blackley
Manchester, M9 8ZS, UK
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Email: daniel.tackley=at=intertekasg.com

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From chemistry-request@ccl.net Fri May 28 06:43:47 2004
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From: "Peter Gannett" <pgannett(at)hsc.wvu.edu>
To: <chemistry(at)ccl.net>, <amber(at)scripps.edu>,
   <ladam(at)smbh.smbh.univ-paris13.fr>
Subject: Re: CCL:Helical parameters extraction from trajectory
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Patrick:

Dials and Windows may help you to do this as it can analyze the entire
trajectory.  See

http://ludwig.chem.wesleyan.edu/~wwang/mdtool/

for information, etc.

Pete Gannett

>>> ladam <ladam(at)smbh.smbh.univ-paris13.fr> 5/27/2004 6:27:21 AM >>>
Hi all,
I would like to extract helical parameters from trajectory files
(in trj or dcd format). As far as I know the only way to do it
is to extract pdb files from the trajectory and analyse them
one by one with the Curves program (R. Lavery). This is rather
painfull when dealing with big trajectories, so I'd like to
know if someone as a trick or a program to extract helical
parameters from trajectories?
Thank you

-- 
------------------------------------------------------------------
| Patrick LADAM                   |                               |
| Laboratoire CSSB                |     THE BIG BANG THEORY:      |
| UFR SMBH                        |                               |
| 74 rue Marcel Cachin            |   In the begining there was   |
| 93017 Bobigny CEDEX             |        nothing at all.        |
| >>> NEW e-mail: <<<             |                               |
| ladam(at)smbh.smbh.univ-paris13.fr |      Then, it exploded...     |
| Tel: 01 48 38 77 26 / 76 85     |                               |
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From chemistry-request@ccl.net Thu May 27 23:38:26 2004
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From: "Asif Rahaman" <Arahaman.-at-.chemdept.chem.ou.edu>
To: <chemistry.-at-.ccl.net>
Subject: CHARMM help needed!
Date: Thu, 27 May 2004 23:41:37 -0500
Message-ID: <000001c4446e$0fbfb5d0$c00d0f81@photo>

Hi all:
   I am doing a gas QM/MM calculation for a molecule (HONO) with CHARMM.
I wanted to see cis-trans conversion in the trajectory. I ran the
calculation at 300K, analyzed the trajectory and found that the dihedral
angle varies +,-30 degrees around the equilibrium 180 degrees. Then I
heated up the system to 800K, calculated the trajectory. This time the
dihedral angle did not change much (+,-35 degree). It is worth while to
mention that AMBER gives flipping of dihedral (cis/trans at 300K). Can
anyone please point out any mistake that I am making??
 I am including my CHARMM input as well as GAMESS input files below.
 
  Thanking you all in advance. With best regards, Asif
 
CHARMM INPUT
-------------------------------------------
* npt
* Test extended system constant pressure and temperature
* dynamics.
*
 
bomlev -2
 
stream datadir.def
 
read rtf card
* TIPS3P WATER TOPOLOGY FILE
*
   28    1
MASS    11 HM1    1.00800 ! Form
MASS    81 OM2   15.99940 ! Form
MASS    61 NM3   14.0079  ! Form
 
MASS    71 OM4   15.9994  ! Form
 
 
RESI HONO    .000
GROUP
 ATOM H1    HM1      0.000  ! Let the charge be zero so no need to
adjust
 ATOM O2    OM2      0.000
 ATOM N3    NM3      0.000
 ATOM O4    OM4      0.000  ! NONB lists for eletrostatics
 
PATC  FIRS NONE LAST NONE
BOND H1 O2  O2 N3  N3 O4
END
 
bomlev -2
read param card
* TIPS3P WATER PARAMETER FILE
*
BOND
H1  O2          0.0       0.9795   ! zero bond term for exclusion of vdw
on Q
O2  N3          0.0       1.4244
N3  O4          0.0       1.1972
 
THETAS
!
NONBONDED   ATOM CDIEL SH
 
NONBONDED   ATOM CDIEL SHIFT VATOM VDISTANCE VSWITCH -
     CUTNB 14.0  CTOFNB 12.0  CTONNB 10.0  EPS 1.0  E14FAC 1.0  WMIN 0.5
!
!HT       0.0       -0.046     0.2245
!OT       0.0       -0.1521    1.7682
 
END
 
bomlev -1
 
! Read in 215 TIP3 solvent molecules and their
! equilibrated coordinates. + 1 QM water
 
READ SEQU HONO 1
GENE NEWM SETU NODIHED
 
OPEN READ UNIT 10 CARD NAME "/home/rasif/wave/500k/hono.crd"
READ COOR UNIT 10 CARD
CLOSE UNIT 10
 
WRITE PSF CARD NAME "/home/rasif/wave/500k/hono.psf"
*psf file for HONO
*
 
! of the box of water.  This value will be used as a scale
! factor for all image transformations.
 
!SET 6 18.856
 
! Open and read the image transformation file for creating
! 26 image objects around the primary structure
 
!CRYSTAL DEFINE CUBIC @6 @6 @6 90.0 90.0 90.0
!CRYSTAL BUILD CUTOFF 18.0 NOPERATIONS 0
 
!IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE RESN TIP3 END
 
 
! Set up GAMESS-US
envi input   "/home/rasif/wave/500k/hono.gms"
envi output  "/home/rasif/wave/500k/hono.gout"
envi punch   "/home/rasif/wave/500k/scratch/hono.punch"
envi dictnry "/home/rasif/wave/500k/scratch/hono.dict"
envi work15  "/home/rasif/wave/500k/scratch/hono.work"
envi dasort  "/home/rasif/wave/500k/scratch/hono.das"
envi DFTGRID "/home/rasif/wave/500k/scratch/hono.dft"
 
! Activate the QM region (STO3G)
GAMESS SELE RESN HONO END REMO
 
mini sd nstep 100
 
open write unit 11 card name "/home/rasif/wave/500k/hono.rst"
open write file unit 12 name "/home/rasif/wave/500k/hono.trj"
open write file unit 13 name "/home/rasif/wave/500k/hono.vel"
 
dynamics leap start time 0.001 nstep 5000 iseed 314159 -
        firstt 800.0 finalt 800.0 tstruc 300.0 -
        twindh 100.0 twindl -100.0 -
        ihbfrq 50 iprfrq 100 nprint 100 isvfrq 100 -
        iasors 0 iasvel 1 ieqfrq 0 -
        nsavc 1 nsavv 1 -
        iunwri 11 iuncrd 12 iunvel 13 -
 
 
STOP
-----------------------
GAMESS input
-------------------
 
$CONTRL COORD=CART NOSYM=1 NPRINT=-5
         SCFTYP=RHF MAXIT=200 ICHARG=0
         RunTyp=gradient
 $END
 $DFT DFTTYP=B3LYP $END
 $BASIS  GBASIS=N31 NGAUSS=6 NDFUNC=1
 $END
 $SCF CONV=1.0d-04 SHIFT=.TRUE. MAXVT=512 $END
 $SYSTEM TIMLIM=5472 MEMORY=1500000 $END
 $SCF    DIRSCF=.True.  $END
 $DATA
 
 $END
 
---------------------
Coordinate file
-----------------------
 
    4
    1    1 HONO H1    -1.72434   0.43654   0.001035
    2    1 HONO O2    -1.04058  -0.26482  -0.000115
    3    1 HONO N3     0.16186   0.49883  -0.000142
    4    1 HONO O4     1.11448  -0.22622   0.000110
---------------------
 
 

From chemistry-request@ccl.net Fri May 28 10:43:56 2004
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Subject: CPMD code  new release   v3.9 .
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Dear  Friends,


version  3.9 is finally ready for distribution.

You can download it from the NEW CPMD web site at www.cpmd.org, were you
can find many additional informations, scripts, pseudopotential libraries
and
 a new searcheable mailing  list archive.

Many new developments, improvements, cleanups, and bug fixes have been
added since the last public version of the code.

Most notably, the methodology for reactive Car-Parrinello metadynamics is
made available in this version.

Other new functionality includes G-space localization of wavefunctions,
Hockney-type Poisson Solver for slabs with influence function in G-Space,
code to determine molecular KS states from Wannier functions, code for
trajectory analysis, calculation of dipole moments using the Berry phase
and in real space, transition matrix elements between orbitals, growth
function for constraints and restraints, new code for applying static
electrical fields, periodic or final diagonalization of WF, and dumping
files for PDOS.

Improvements of the code include performance and OpenMP improvements,
improved code for keeping wavefunction in real space, updated TDDFT, SAOP
TDDFT functional, a much improved configure script, bug fixes for HF
exchange, screened exchange, cleanup of memory management, more checks on
unsupported options, fixed constraints in geometry optimization.


Happy computing!

The CPMD Team

















From chemistry-request@ccl.net Fri May 28 16:56:29 2004
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Date: Fri, 28 May 2004 17:59:34 -0400
From: "Renxiao Wang" <renxiao/at/med.umich.edu>
To: <chemistry/at/ccl.net>
Subject: Annoucement: The PDBbind database is available now
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Dear Researchers,

We would like to announce the release of the PDBbind database. This
database, which is public-accessible at http://www.pdbbind.org/, is
designed to provide a collection of binding affinity data for the
protein-ligand complexes on the whole PDB level. Its current contents
include binding affinity data (Kd, Ki, & IC50) for nearly 1500
protein-ligand complexes. The development of this database is described
in a recently published paper on J. Med. Chem., 2004, 47(12),
2977-2980.

Academic and governmental users may access the full contents of this
database for free; while industrial users may do so with a moderate
amount of subscription fee. Please follow the instructions on the
PDBbind web site to register.

We wish this database will help with a wide range of docking/scoring
studies. We will work very hard to maintain and update this database.

Best regards,

Renxiao



--------------------------------------------------------------------------------------------------
Renxiao Wang, Ph.D.
Research Investigator
Department of Internal Medicine, Hematology/Oncology Division
University of Michigan Medical School
Ann Arbor, MI 48109, U.S.A.
Tel: (734) 764-2449; Fax: (734) 764-2532
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From chemistry-request@ccl.net Fri May 28 19:55:07 2004
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	Fri, 28 May 2004 20:58:17 -0400
Date: Fri, 28 May 2004 20:58:17 -0400
From: Chi-Yuan Chen <chenca{at}email.uc.edu>
Subject: Question about NAMD !!
To: Computational Chemistry List<chemistry{at}ccl.net>
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Dear sirs:

Regarding NAMD, the force field for nonbonded interactions is 
basically the pariwise potential model, but it's often not 
suitable for transition metals.

Howerver, it always involves transition metals in the 
biosystems, like oxygen delivery and hemoglobin building.

Can we still apply NAMD in this kind of systems?why?
if not, is there any suitable program for huge biosystem 
involved transition metals? 

thanks in advance,
Sincerely,


Chi-Yuan Chen
Graduate Student

Center for Computer-Aided Molecular Design
Department of Chemical and Materials Engineering
University of Cincinnati
Cincinnati, Ohio 45221-0171
Email: chenca{at}email.uc.edu


From chemistry-request@ccl.net Fri May 28 10:24:21 2004
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Date: Fri, 28 May 2004 17:32:52 +0200
From: Alessandro Contini <alessandro.contini!at!unimi.it>
Subject: Re: CCL:Molekel and G03
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Dear Daniel,
I also faced the same problem, however I didn't solved it. I contacted last 
year the group of CSCS for an analogue reason (upgrading of GAMESS) and the 
suddenly replied giving me a new corrected executable, that later was 
published on their site.
You could however deeply analyze g03 output using Molden (http://
www.caos.kun.nl/~schaft/molden/molden.html), it does a really good job 

Hope this help

Alessandro

Alle 15:31, venerdl 28 maggio 2004, Tackley Daniel R - INTE ha scritto:
> Hi All,
>
> I have been using Molekel in conjunction with G98 for the last couple of
> years and have been very happy with the quality of analysis that I have
> been able to achieve with this combination.
>
> The upgrade from G98 to G03 has led to a few problems, most of which arise
>
> > from the slightly updated layout of the new G03 output file. The main
>
> problems seem to come from the geometry section since on opening the output
> file, the molecule in Molekel comes out flattened into 2-dimensions. I can
> still manage most visualisations by using cube files but the one analysis
> that is not possible is that of vibrational modes. This data can only be
> obtained from the G03 output file.
>
> I've tried contacting CSCS (Swiss National Supercomputing Centre) who hold
> the rights but their (automated) respone was that they aren't providing any
> support. Attempts to get hold of the source code to try to correct it
> myself also failed.
>
> Does anyone have any suggestions on:
>
> 1. Has anyone else solved this problem?
>
> 2. How I might get access to the source code for Molekel?
>
> 3. Any other programs that I could use to visualise vibrational modes
> (animations and vectors if possible)
>
>
> Thanks for your help,
>
> Daniel Tackley
>
> --
> Dr Daniel Tackley
> Computational Chemistry Group
> Intertek ASG
> PO Box 42
> Hexagon House
> Blackley
> Manchester, M9 8ZS, UK
> Tel: +44 (0)161 721 2541
> Email: daniel.tackley!at!intertekasg.com
>
> CONFIDENTIALITY NOTICE: The information contained in this electronic
> message is intended ONLY for the confidential use of the above named
> recipient(s) and may be subject to legal privilege. If the reader of this
> message is not the intended recipient(s) or person responsible for
> delivering it to the intended recipient(s), you are hereby notified that
> you have received this communication in error and that any review,
> dissemination, distribution, copying or use of this communication or the
> information in it is strictly prohibited. If you have received this in
> error, please notify the sender immediately by electronic mail at the
> sender's address set forth above and destroy this electronic message. Thank
> you.
>
>
>
> -= This is automatically added to each message by the mailing script =-
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> line and send your message to:  CHEMISTRY!at!ccl.net
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-- 
Alessandro Contini, Ph.D.
Istituto di Chimica Organica "Alessandro Marchesini"
Universit` degli Studi di Milano, Facolt` di Farmacia
Via Venezian, 21 20133 Milano 
Tel. +390250314480 Fax. +390250314476
e-mail alessandro.contini!at!unimi.it





From chemistry-request@ccl.net Fri May 28 10:26:58 2004
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Date: Fri, 28 May 2004 17:28:42 +0200
From: Marcin Dulak <Marcin_Dulak^at^poczta.onet.pl>
Subject: Re: CCL:Molekel and G03
In-reply-to: <1BF03EF442B58445A3221497213311D701D87E78@UKHX21>
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Dear Daniel,

Change the line in the g03 output file from:
"Gaussian 03:  x86-Linux-G03RevB.03 4-May-2003"
 (or the one corresponding to your system), into
"Gaussian 98:  x86-Linux-G03RevB.03 4-May-2003"

Marcin

Tackley Daniel R - INTE wrote:

>Hi All,
>
>I have been using Molekel in conjunction with G98 for the last couple of
>years and have been very happy with the quality of analysis that I have been
>able to achieve with this combination.
>
>The upgrade from G98 to G03 has led to a few problems, most of which arise
>  
>
>>from the slightly updated layout of the new G03 output file. The main
>>    
>>
>problems seem to come from the geometry section since on opening the output
>file, the molecule in Molekel comes out flattened into 2-dimensions. I can
>still manage most visualisations by using cube files but the one analysis
>that is not possible is that of vibrational modes. This data can only be
>obtained from the G03 output file.
>
>I've tried contacting CSCS (Swiss National Supercomputing Centre) who hold
>the rights but their (automated) respone was that they aren't providing any
>support. Attempts to get hold of the source code to try to correct it myself
>also failed.
>
>Does anyone have any suggestions on:
>
>1. Has anyone else solved this problem?
>
>2. How I might get access to the source code for Molekel?
>
>3. Any other programs that I could use to visualise vibrational modes
>(animations and vectors if possible)
>
>
>Thanks for your help,
>
>Daniel Tackley
>
>--
>Dr Daniel Tackley
>Computational Chemistry Group
>Intertek ASG
>PO Box 42
>Hexagon House
>Blackley
>Manchester, M9 8ZS, UK
>Tel: +44 (0)161 721 2541
>Email: daniel.tackley^at^intertekasg.com
>
>CONFIDENTIALITY NOTICE: The information contained in this electronic message
>is intended ONLY for the confidential use of the above named recipient(s)
>and may be subject to legal privilege. If the reader of this message is not
>the intended recipient(s) or person responsible for delivering it to the
>intended recipient(s), you are hereby notified that you have received this
>communication in error and that any review, dissemination, distribution,
>copying or use of this communication or the information in it is strictly
>prohibited. If you have received this in error, please notify the sender
>immediately by electronic mail at the sender's address set forth above and
>destroy this electronic message. Thank you.
>
>
>
>-= This is automatically added to each message by the mailing script =-
>To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
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>
>
>
>
>
>
>  
>

-- 
**********************************
 
Marcin Dulak
email: Marcin_Dulak^at^poczta.onet.pl

**********************************

fortune says:

When you don't know what you are doing, do it neatly.


--Boundary_(ID_p1xjhlfu81uquAd+C/0JbQ)
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</head>
<body bgcolor="#ffffff" text="#000000">
Dear Daniel,<br>
<br>
Change the line in the g03 output file from:<br>
"Gaussian 03:&nbsp; x86-Linux-G03RevB.03 4-May-2003"<br>
&nbsp;(or the one corresponding to your system), into<br>
"Gaussian 98:&nbsp; x86-Linux-G03RevB.03 4-May-2003"<br>
<br>
Marcin<br>
<br>
Tackley Daniel R - INTE wrote:
<blockquote cite="mid1BF03EF442B58445A3221497213311D701D87E78@UKHX21"
 type="cite">
  <pre wrap="">Hi All,

I have been using Molekel in conjunction with G98 for the last couple of
years and have been very happy with the quality of analysis that I have been
able to achieve with this combination.

The upgrade from G98 to G03 has led to a few problems, most of which arise
  </pre>
  <blockquote type="cite">
    <pre wrap="">from the slightly updated layout of the new G03 output file. The main
    </pre>
  </blockquote>
  <pre wrap=""><!---->problems seem to come from the geometry section since on opening the output
file, the molecule in Molekel comes out flattened into 2-dimensions. I can
still manage most visualisations by using cube files but the one analysis
that is not possible is that of vibrational modes. This data can only be
obtained from the G03 output file.

I've tried contacting CSCS (Swiss National Supercomputing Centre) who hold
the rights but their (automated) respone was that they aren't providing any
support. Attempts to get hold of the source code to try to correct it myself
also failed.

Does anyone have any suggestions on:

1. Has anyone else solved this problem?

2. How I might get access to the source code for Molekel?

3. Any other programs that I could use to visualise vibrational modes
(animations and vectors if possible)


Thanks for your help,

Daniel Tackley

--
Dr Daniel Tackley
Computational Chemistry Group
Intertek ASG
PO Box 42
Hexagon House
Blackley
Manchester, M9 8ZS, UK
Tel: +44 (0)161 721 2541
Email: <a class="moz-txt-link-abbreviated" href="mailto:daniel.tackley^at^intertekasg.com">daniel.tackley^at^intertekasg.com</a>

CONFIDENTIALITY NOTICE: The information contained in this electronic message
is intended ONLY for the confidential use of the above named recipient(s)
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the intended recipient(s) or person responsible for delivering it to the
intended recipient(s), you are hereby notified that you have received this
communication in error and that any review, dissemination, distribution,
copying or use of this communication or the information in it is strictly
prohibited. If you have received this in error, please notify the sender
immediately by electronic mail at the sender's address set forth above and
destroy this electronic message. Thank you.



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  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
**********************************
 
Marcin Dulak
email: <a class="moz-txt-link-abbreviated" href="mailto:Marcin_Dulak^at^poczta.onet.pl">Marcin_Dulak^at^poczta.onet.pl</a>

**********************************

fortune says:

When you don't know what you are doing, do it neatly.
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Dear Colleagues:

I  would  like to announce the 4th version of the Workshop of
Computational Chemistry and Molecular Spectroscopy to be held during
October 19-22 in Punta de Tralca, Chile.  Punta de Tralca is a beatiful
beach located about 80 miles west from Santiago, and next to Isla Negra =
(where is Neruda's musseum).=20
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please visit our WeB page at:  www.unab.cl/workshop

For more information, please contact

Ramiro Arratia-P=E9rez
Director, Depto. de Ciencias Quimicas
Facultad de Ecologia y Recursos Naturales
Universidad Andr=E9s Bello
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<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
size=3D3>I&nbsp;=20
would&nbsp; like to announce the 4th version of the Workshop =
of<BR>Computational=20
Chemistry and Molecular Spectroscopy to be held during<BR>October 19-22 =
in Punta=20
de Tralca, Chile.&nbsp; Punta de Tralca is a beatiful<BR>beach located =
about 80=20
miles west from Santiago, and next to Isla Negra (where is Neruda's =
musseum).=20
</FONT></FONT></DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
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<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
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Naturales<BR>Universidad=20
Andr=E9s Bello<BR>Republica 275, Santiago<BR>Fono: =
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<DIV>&nbsp;</DIV>
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