Re: [AMBER] MMPBSA Molsurf vs LCPO

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 20 Jan 2015 11:01:31 -0800

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Jan 20 2015 - 11:30:04 PST