[gmx-users] FEP charged molecule cuestion

David Mobley dmobley at gmail.com
Sun Aug 21 12:37:38 CEST 2011

This is a tough issue and there are some unresolved questions here.

I recommend seeing the work of Kastenholz and Hunenberger on ion solvation
in JCP a couple years ago (two companion papers) as these explain the key


On Wed, Aug 17, 2011 at 3:24 AM, Marcelino Arciniega Castro <
macastro at mytum.de> wrote:

> Hi there,
> Could someone please share some ideas about the next situation?:
> I am trying to estimate the relative binding affinity of two small
> molecules to a protein. In the setup process, ions are added in the solvent
> to neutralize the system. Then as everybody suggest, the ligand partial
> charges should be decouple to zero. But my specific case, the small
> molecules are charged, that means that after turning off the ligand partial
> charges, the system will have a net charge (because the ions in the
> solvent). Turning off the ions charges does not solve the problem, because
> of the protein charges.
> The concrete question are:
> Should I continue to atom mutation step using PME in a non-neutral system?
> It would make sense to turn off the partial charges of the some atoms in
> the small molecule (just those that are going to be mutated)?
> Thanks in advance
> Marcelino
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David Mobley
dmobley at gmail.com
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