VMD-L Mailing List

From: rodolfo gonzalez (rodogonza234_at_gmail.com)
Date: Mon Oct 21 2013 - 10:43:01 CDT

Ok, for example if I wanted to parametrize a chlorobenzene and lets assume
that the paramchem penalties on all the atoms is below 10 except for the
Chlorine atom and the Carbon next to it. Then I would think that except for
these two atoms, the rest are similar to the corresponding ones in benzene,
and I would be tempted to keep the charges proposed by paramchem for those
atoms while trying to parametrize only the ones with high penalty. Does it
make any sense?

Thanks

On 21 October 2013 13:59, Norman Geist <norman.geist_at_uni-greifswald.de>wrote:

> 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 ****
>
> ** **
>