Re: [AMBER] MMPBSA Molsurf vs LCPO

From: Aronica, Pietro <>
Date: Tue, 20 Jan 2015 19:39:02 +0000

Thank you very much.
Follow up question: what happened to inp? Whenever I use inp=2, I get wildly inconsistent results, for example ranging from -9 to +75 to +110 for a system that should have around -110. In fact, I cannot reproduce the results of the MMPBSA tutorial on the website if I use inp=2. inp=1, on the other hand, gives more "reasonable" results and can reproduce the tutorial. Is there a specific combination of parameters I should be using with inp=2? Because just taking the sample input file from the tutorial does not seem to work.
Kind regards

-----Original Message-----
From: Ray Luo, Ph.D. []
Sent: 20 January 2015 19:02
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA Molsurf vs LCPO


The newer python scripts no longer use molsurf for pb surface calculation.
Instead, it uses the built-in numerical routine of pbsa. You can check the agreement between the numerical surface routine and molsurf by yourself.
They agree with each other extremely well since both are brute-force numerical methods strictly following the SAS definition.They are very different from LCPO, which is a pairwise approximated method.

All the best,

Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900
On Tue, Jan 20, 2015 at 10:43 AM, Aronica, Pietro <> wrote:
> Hello,
> In, is Molsurf or LCPO used to calculate the SASA? With GB, 
> there is a flag to choose this, but this is absent in PB. The manual 
> suggests that Molsurf is correct for PB calculations, so I was 
> wondering if that was the default.
> Kind regards
> Pietro
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Received on Tue Jan 20 2015 - 12:00:03 PST
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