VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Feb 19 2020 - 10:47:26 CST

Hi David, assuming that this is for the CHARMM force field (is it?), you
should be checking its literature papers and forum.

In general, it is always a good idea to include more data points as
constraints for the parameter optimization, but the specifics depend on the
choice of force field and the molecule under study.

Giacomo

On Wed, Feb 19, 2020 at 11:35 AM David Sáez <davidsaezsan_at_gmail.com> wrote:

> Dear community,
>
> When calculating charges for a thioester o ester compounds the plugin
> places water molecules in front of hydrogens (correct according to
> tutorial), oxygens (correct according to tutorial) and also the carbonylic
> carbon atom (C*=O). Is this correct according to the parametrization
> protocol, or should I remove the last water molecule?
>
>
> Thanks.
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin