From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Oct 21 2013 - 12:53:59 CDT
The recommended workflow for applying CGenFF to a general organic molecule
would probably be something like this:
- Submit the whole molecule to the CGenFF program at paramchem.org
- Look closely at the output and penalties
- If optimization seems to be required, split the molecule into relevant
fragments/groups (more information:
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=32799&#Post32799
)
- Assuming the high charge penalties don't occur at an interface between
fragments (see CHARMM forum discussion above), submit the individual
fragments that require optimization to the CGenFF program again.
- Assuming the fragments still have high penalties, optimize the charges,
that is, *all* the charges using *all* the water interactions, as Norman
explained. To corroborate, transferability of charges is typically
acceptable between different occurrences of the same *chemical group*, but
not between different occurrences of the same *atom type*, and
accordingly, the CGenFF program can often be observed to assign vastly
different charges to the same atom type in different chemical groups. The
algorithm behind this has been published.
On 10/21/2013 02:57 AM, rodolfo gonzalez wrote:
> 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
> <mailto: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
>
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