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

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Wed, 08 Aug 2012 07:45:05 +0200

Hi Ray,

Thank you very much for all your clarifications. We need to estimate the entropic contribution before we can say which method provides more reasonable numbers. We will play around a bit with different methods.

Best,
Vlad

---
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
"Ray Luo, Ph.D." <ray.luo.uci.edu> wrote:
Indeed, there can be huge difference in delta G between different
nonpolar solvent models. That was why the inp=2 method was developed
in the first place. It is apparently which number is more reasonable
in your test case.
Nevertheless, what is less scientifically challenging, though, is to
look at the delta delta G's ... The differences are often much smaller
between different methods.
Ray
On Tue, Aug 7, 2012 at 10:04 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> 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
> Vlad
> ---
> 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 - 23:00:03 PDT