Re: [AMBER] binding energy calculations

From: case <>
Date: Fri, 6 Apr 2012 21:04:59 -0400

On Fri, Apr 06, 2012, kirtana S wrote:
> My system consists of a polymer molecule in explicit water(TIP3P) with
> ions. Using MMGBSA I have to use a vacuum trajectory and topology files of
> each ligand and receptor.
> Now to calculate the binding free energy of solvent with the polymer
> molecule how should I go about.

It's not clear what energy you want: there would not ordinarily be a "binding
free energy" between a polymer and solvent. Or at least, you would have to
define this carefully.

One could estimate the transfer free energy between gas phase and water, which
would be something like a free energy of interaction between the two. But this
is not often an interesting value per se, since it generally can't be measured.


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Received on Fri Apr 06 2012 - 18:30:03 PDT
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