Re: [AMBER] solvation free energy

From: kirtana S <>
Date: Tue, 14 Oct 2014 00:53:58 -0400

As I understand to calculate the solvation energy I have to use PBSA to
calculate the polar solvation energy. To estimate the non-polar part of
solvation energy I have to use SASA + Vander Waals interaction energy
between solute and solvent atoms.
My question is about the type of files I will use to calculate this, i.e
the prmtop and inpcrd file. Do I need to solvate it or use continuum
solvent model.


On Sun, Oct 12, 2014 at 4:44 PM, David A Case <>

> On Sun, Oct 12, 2014, kirtana S wrote:
> >
> > Thank you. I do not want to use this information for any other purpose.
> My
> > main purpose is to obtain the solvation free energy. Do I need to set up
> a
> > simulation in implicit solvent conditions.There were some issues related
> to
> > running PB calculations as the dihedral phase was zero. Can you suggest
> me
> > other alternatives.
> You should report what the "dihedral phase was zero" problem was in detail.
> This should have nothing to do with PB calculations.
> My *guess* is that PB solvation with the simple version of non-polar
> solvation is likely to give the most interpretable results. Since there
> are no relevant experiments, there is no good indication that I know of
> concerning how accurate one should expect the result to be.
> ....dac
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Received on Mon Oct 13 2014 - 22:00:02 PDT
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