From: Sajad Falsafi-Zadeh (sajad.falsafi_at_yahoo.com)
Date: Fri May 25 2012 - 01:50:35 CDT
Hi,
I assume you want to generate PSF file for a new molecule but not non-standard amino acid. you can use the topotools plug-in.
here i write a script to generate PSF file via topotools plug-in.
package require topotools
mol new YOURPDB.pdb
topo retypebonds
topo guessangles
topo guessdihedrals
topo guessimpropers
set sel [atomselect top all]
$sel writepdb NEW.pdb
$sel writepsf NEW.psf
Â
Best of luck,
Sajad Falsafi
Bioinformatics unit, Dept. of Genetics, Shahid Chamran University of Ahvaz
>________________________________
> From: Norman Geist <norman.geist_at_uni-greifswald.de>
>To: 'MOHAMMAD JAVAD AGHAEI' <mj_aghaei_at_aut.ac.ir>
>Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
>Sent: Friday, May 25, 2012 10:26 AM
>Subject: AW: AW: namd-l: Generating force field for novel molecules
>
>
>
>Hi,
>Â
>if I remember correctly, there was a post to this list about the
release of a tool called paratool, with it, it should be possible to generate
force field parameters for charmm and I’m sure there are a lot of tutorials for
it.
>Â
>If you read through some papers you will see that generating all
ff parameters by yourself can however be a project itself and too time
consuming. Often people only compute the partial charges of their molecules
with this QM and use the other parameters from publications and similar
molecules. If your molecule doesn’t contain anything special, that would be the
best thing I guess. If it is really special, you should search for published
parameters. Also, if you try to generate all parameters from the ground up, you
will have to verify them in many tests. The bottom line is, generating a full
set of parameters is too much work, especially for torsion angles if you have
sugars or similar.
>Â
>The standard procedure for amber partial charges and  ff type
guessing is pretty easy.
>1.      Gaussian/Gamess energy
optimization
>2.      Gaussian/Gamess electro
static potential
>3.      Antechamber
>4.      Some after work if force
field typing mistakes
>-> http://www.teokem.lu.se/~ulf/Methods/resp.html
>For charm, I would inform about that paratool.
>Â
>Please remember that you always should know what you are doing.
I will not help you to only follow tutorials to generate parameters that you
don’t understand. Quantum mechanics is the base of force field, so it won’t
harm to know it a little.
>Â
>Norman Geist.
>Â
>Von:MOHAMMAD JAVAD
AGHAEI [mailto:mj_aghaei_at_aut.ac.ir]
>Gesendet: Donnerstag, 24. Mai 2012 09:35
>An: Norman Geist
>Betreff: Re: AW: namd-l: Generating force field for novel molecules
>Â
>Hi
Noramn
>
>Thanks a lot for your appreciation. Basically I work with CHARMM; but I have no
problem switching to AMBER, since NAMD supports that one too. I have done some
MD simulations;Â but I'm new to the field of quantum chemistry. I'd be
grateful if you provided me with some tutorials about the method you mentioned
(using antechamber after gaussian). I found some tutorials on the antechamber
website, but they're too specific and lack educational and explanatory fashion
(I'm looking for something like NAMD tutorials which are so great). By the way,
some keywords or web links would also work, since I don't want to bother you
too much.
>
>Best Regards
>Mohammad Javad Aghaei
>AmirKabir University of Technology
>Tehran, Iran
>mj_aghaei_at_aut.ac.ir
>
>P.S. It would also be so nice of you to share any ideas about generating CHARMM
force-field parameters.
>
>On Thu, 05/24/2012 08:45 AM,
"Norman Geist" <norman.geist_at_uni-greifswald.de>
wrote:
>Hi Mohammad,
>Â
>for
which force field you want to generate these parameters, that’s really
important, as the procedure is mostly different. For amber one could easily use
Gaussian or Games or the RED SERVER which provide both, and then put it through
antechamber afterwards. For charmm there’s a different procedure. But I think
you would find many tutorials for that on the net. If you already know that
all, and the problem is about this special kind of molecules, please tell what
the problem with it really is.
>Â
>Norman
Geist.
>Â
>Von:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von MOHAMMAD
JAVAD AGHAEI
>Gesendet: Mittwoch, 23. Mai 2012 10:17
>An: namd-l_at_ks.uiuc.edu
>Betreff: namd-l: Generating force field for novel molecules
>Â
>​Hi all
>
>Does anyone have any experience in generating force field parameters for novel
small molecules (e.g. morphine) using quantum mechanics softwares
(semi-empirical or ab-initio).
>If so, it would be so nice of them to share their experience.
>
>Best Regards
>Mohammad Javad Aghaei
>AmirKabir University of Technology
>Tehran, Iran
>mj_aghaei_at_aut.ac.ir
>--
>This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
>
>
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