AMBER Archive (2009)

Subject: Re: [AMBER] The hydrophobic contribution

From: case (
Date: Thu Oct 08 2009 - 07:41:28 CDT

On Thu, Oct 08, 2009, Rilei Yu wrote:
> Here I am really appreciated for your help all the time. Now, I still
> have a problem, the amber cannot be installed in the cluster of our
> institute but on my private computer. I want to calculate the binding
> free energy of my protein complex. I have used apbs to calculate the
> electrostatic contributions, and now I want to calculate the hydrophobic
> contributions, do anyone here, know how can I do this job, can amber do
> this? I just want calculate the binding energy from 10 frames for one
> complex, I have more than 40 complexes, I can hardly calculate them one
> by one by run long time MM/PBAS.

You can use the molsurf program to compute the solvent accessible surface area
for the ligand, protein and complex, get the change in SASA from these, and
multiply by some "magic factor" to get an estimate of the nonpolar
contribution to binding. The mm_pbsa script can automate this for you.


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