Re: [AMBER] MMPBSA Molsurf vs LCPO

From: Ray Luo, Ph.D. <ray.luo.uci.edu> Date: Tue, 20 Jan 2015 12:06:11 -0800

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Jan 20, 2015 at 11:39 AM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> 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
> Pietro
>
> -----Original Message-----
> From: Ray Luo, Ph.D. [mailto:ray.luo.uci.edu]
> Sent: 20 January 2015 19:02
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA Molsurf vs LCPO
>
> Pietro,
>
> 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
>
> --
> Ray Luo, Ph.D.
> Professor,
> 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 <
> pietro.aronica07.imperial.ac.uk> wrote:
>
> > Hello,
> > In MMPBSA.py, 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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