Re: AW: AW: Generating force field for novel molecules

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 25 2012 - 05:44:42 CDT

On Fri, May 25, 2012 at 2:50 AM, Sajad Falsafi-Zadeh
<sajad.falsafi_at_yahoo.com> wrote:
> 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

that is a useless exercise, since this procedure
neither assigns the necessary partial charges,
atom types and for certain does not allow the
calculation to run, if there are no suitable bonded
or non-bonded parameters for the hypothetical
atom types or the molecule. finding the parameters
is the "hard" work, not the topology. ...and it cannot
be entirely automated, but requires human interaction
and common sense.

axel.

>
>
> 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,
>
> 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 Iím sure there are a lot of tutorials for
> it.
>
> 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 doesnít 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.
>
> 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.
>
> 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 donít
> understand. Quantum mechanics is the base of force field, so it wonít harm
> to know it a little.
>
> Norman Geist.
>
> 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
>
> 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;† 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,
>
> for which force field you want to generate these parameters, thatís 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 thereís 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.
>
> Norman Geist.
>
> 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
>
> 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
>
> --
>
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>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.comhttp://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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