Re: [AMBER] solvation free energy

From: David A Case <>
Date: Sun, 12 Oct 2014 16:44:03 -0400

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.


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Received on Sun Oct 12 2014 - 14:00:02 PDT
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