Re: vmd-l: fftk-charges

From: rodolfo gonzalez (rodogonza234_at_gmail.com)
Date: Mon Oct 21 2013 - 01:57:55 CDT

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 donít 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 ****
>

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