From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Feb 20 2020 - 08:10:32 CST

David,

You tell us! Apparently at some point, we thought this was a good idea to place a water there. If you find contradictory information in the literature, please let us know!

To be honest though, one of the things parametrizing multiple molecules has taught us is that it’s not as “cookbook” as we initially thought.

Best,
JC

> On Feb 19, 2020, at 11:47 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> 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 <mailto: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 <http://goo.gl/Q3TBQU>
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>