Re: [AMBER] binding energy calculations

From: David A Case <>
Date: Mon, 9 Apr 2012 16:38:44 -0400

On Mon, Apr 09, 2012, kirtana S wrote:

> Will this give meaningful results if I use the trajectory obtained from the
> explicit water simulations by removing water and using nobox to obtain my
> new trajectory.
> And use a vacuum topology file of the polymer by itself .
> Can I obtain the solvation free energy using MMPBSA.

The "PBSA" part of mmpbsa will estimate the solvation free energy of each
snapshot you save, and the "MM" part will average over snapshots. So the
general answer is "yes" you should be able to use mm-pbsa to get an average
solvation free energy. You could then do it again with a different ionic
strength to get some feeling for the effect of ionic strength on solvation
free energy. To the extent that PB theory "works", these estimates may be
helpful, (although it is still somewhat unclear to me what one would do with
such numbers once they were computed.)


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Received on Mon Apr 09 2012 - 14:00:05 PDT
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