Re: [AMBER] binding energy calculations

From: Jason Swails <>
Date: Tue, 10 Apr 2012 00:33:49 -0400

On Apr 9, 2012, at 9:33 PM, kirtana S <> wrote:

> I used sander with igb=10 ( to activate pbsa calculation as in manual) with
> vacuum trajectory with ions and solvent removed.
> &cntrl
> imin=5,
> gbsa=1,

PBSA calculates the non-polar energies on its own, so there is no need to set gbsa=1 here.

What is happening is the surface area is being calculated twice.

I would suggest looking through the pbsa section of the manual for details about available pbsa parameters (or using to create a sample input file.

> surften=1,

This sets the surface tension to 1. Therefore, the esurf and enpolar will be the LCPO-calculated SASA, to which you have to multiply your real surface tension (e.g., 0.0072 is used for calculations in GB solvent) in order to get non-polar energies.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Apr 09 2012 - 22:00:04 PDT
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