[AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Tue, 07 Aug 2012 19:04:50 +0200

Dear all,

We performed MMPBSA to estimate the binding affinity of a protein to DNA.

We did some tests using the linear PB and different methods for estimating the nonpolar solvation free energy (inp=1 versus inp=2).

When comparing the results we got for the enthalpic contribution -13 kcal/mol with inp=2 and -294 kcal/mol with inp=1.

This difference seems huge to me and I would like to ask if amybody else had observed such large differences between the 2 methods to estimate the non-polar solvation free energy? If yes, is there any good reason why we see these differences?

We are using Amber 12 with Amber Tools 12.

Thank you for any advice on this.

Best wishes
Dr. Vlad Cojocaru
Max Planck Institute Muenster
Roentgenstrasse 20,
48149 Muenster, Germany
Tel: +49-251-70365324
Sent from my mobile phone; Sorry for being short and for any errors
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Received on Tue Aug 07 2012 - 10:30:02 PDT
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