VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Oct 21 2013 - 07:59:53 CDT

What do you define as similar atoms?

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
rodolfo gonzalez
Gesendet: Montag, 21. Oktober 2013 08:58
An: Norman Geist
Cc: Namd Mailing List; vmd-l_at_ks.uiuc.edu
Betreff: Re: vmd-l: fftk-charges

 

Hi,

Thanks a lot for your answer. I understand the point about the importance of
the specific environment on the atomic charges of each molecule. However, I
thought that for transferability reasons and for keeping consistency with
the rest of the compounds in the CGenFF the charges of similar atoms should
be kept the same. Isn't that the reason why the server paramchem provides
penalties when looking for homologous parameters for a new compound?

Thanks again for your reply, as I am new to this procedures, this kind of
discussions are really helpful.

 

On 21 October 2013 07:23, Norman Geist <norman.geist_at_uni-greifswald.de>
wrote:

Hi,

 

I don't know if this is different in the charmm ff, but usually the partial
charges are specific for compounds, or better called residues and not for
atom types. Therefore one would usually compute the partial charges for a
new residue from scratch for the whole molecule. I might be wrong here, but
the partial charges depend a lot or almost only on the chemical environment.
Means taking the charges from different molecules having a different
chemical environment , is IMHO wrong.

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
rodolfo gonzalez
Gesendet: Sonntag, 20. Oktober 2013 17:01
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: fftk-charges

 

Hi,

I am trying to parametrize a compound for which most atomic partial charges
are already available in the CGenFF except for a few atoms. My question is:
do I need to run the QM water-compund calculations for all the H-bond donors
or acceptors atoms in my molecule or only for those whose atomic charge need
to be parametrized?

Thanks,

Regards