VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Sep 09 2015 - 09:42:24 CDT

Van,

The COLP tool is best way to inspect the ability of the MM charges to reproduce the QM target data. It will provide insight into the performance of the entire molecule, as well as, break out the individual interactions. There is currently no user guide for this tool, although we plan to add this material to an ffTK tutorial (currently being written).

After completing the parameterization, it is advisable to benchmark the parameters against experimentally measured quantities (e.g., free energy of solvation). Unfortunately, these are not always available for the molecule of interest.

Regards,
Christopher Mayne

On Sep 9, 2015, at 4:58 AM, fvlieffe wrote:

> hi everyone,
>
> I'm working on 2 different molecules, a positively charge molecule with an aromatic five membered ring (containing a positively charged nitrogen)
> and a substitued pyrimidine;
> After running successfully several times the charge optimization step of the fftk (following the tutorial), I get some partial charges
> (quite similar between the several try I did) but these charges are for some of them really high (near 1).
>
> Is there any tool to validate these charges?
> And is there an user guide for the COLP tool?
>
> thank you
>
> --
> Van Liefferinge François
> Phd Student in Chemistry
> S.F.M.B., Université Libre de Bruxelles
> Campus Plaine CP 206/2
> Bâtiment BC, local 1C4.107
> Blvd. du Triomphe
> B-1050 Bruxelles
> BELGIQUE
>