Re: [AMBER] Estimation of free energy of solvation ?

From: <>
Date: Wed, 15 Jun 2011 11:36:21 -0400 (EDT)

Hi Marek,

> But this is not my case. Having significant part of molecule hydrophobic
> there is significant change
> in molecular structure upon it's solvation so the change in internal
> energy (EL., VDW, bond ...) is not
> negligible comparing to solvent-solute part.

I see... For that system, using MMPBSA makes sense of course. What I was
trying to say before is, if your molecule changes shape a lot during
solvation, it is quite likely that the forcefield will not give you a good
conformational ensemble for the vacuum state, to give just one example,
partial charges are derived specifically for the solvated system.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Jun 15 2011 - 09:00:04 PDT
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