From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Fri May 25 2012 - 09:34:11 CDT
The methodology for developing CHARMM parameters is well described here:
http://mackerell.umaryland.edu/~kenno/tutorial/
<http://mackerell.umaryland.edu/%7Ekenno/tutorial/>
One has to be very careful with automated force field development tools,
including antechamber. There are a lot of "special cases" where
everything looks right (the calculations ran fine), but the results are
totally wrong.
Jeff
On 5/25/2012 1:56 AM, Norman Geist wrote:
>
> 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 I’m 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 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.
>
> 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
> don’t understand. Quantum mechanics is the base of force field, so it
> won’t 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, 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.
>
> 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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-- ================================================================= Jeffrey J. Potoff jpotoff_at_wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu =================================================================
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