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

From: Marek Maly <>
Date: Wed, 15 Jun 2011 17:12:41 +0200

Dear Thomas,

If I am not wrong, your suggestion is OK for molecules which do not change
their shape upon solvation. In that case I agree that enthalpic part
(probably usually dominant)
of the solvation energy is possible to reduce just on interaction energy
between solute and solvent
(polar + hydrophobic contribution) which might be calculated with several
PB or GB solvers with
extension to calculate hydrophobic (nonpolar) contribution which might be
usually also neglected in case
of charged molecules.

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.

BTW my question was related to specific entropy part (importance,
eventual. calculation) connected with
creation of cavity, reorganization of the solvent around the solute
surface etc.

But anyway thank you very much for your response !

      Best wishes,


Dne Wed, 15 Jun 2011 16:58:10 +0200 <> napsal/-a:

> Dear Marek,
>>> I am just thinking about the possibility of calculating
>>> free energy of solvation for the given molecule using MM/PBSA.
>>> Let say that I have (i) MD trajectory of the given molecule from
>>> simulation in vacuum and
>>> (ii) MD trajectory from simulation of the same molecule in explicit
>>> water.
>>> If I am not wrong, enthalpic contribution to the complete solvation
>>> energy
>>> could be estimated like:
>>> H(solvated molecule) - H(molecule simulated in vacuum)
>>> ( where H(solvated molecule) contains also interaction energy with
>>> solvent
>>> )
> why not just use pbsa (in sander?) or delphi as a standalone program? It
> should give you the free energy of solvation for your molecule, maybe
> based on some MD snapshots. Using MMPBSA for the analysis would just add
> the change in internal FF-energy upon transferring the molecule to
> vacuum,
> which would not be very accurate in any case.
> Thomas
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
> _______________________________________________
> AMBER mailing list

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Received on Wed Jun 15 2011 - 08:30:06 PDT
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