AMBER Archive (2003)

Subject: Re: AMBER: surften value in mm_gbsa/mm_pbsa calculations

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Sep 02 2003 - 15:30:15 CDT

"Sergio E. Wong" wrote:
>
> Dear sirs;
>
> I'm running amber 7 on a linux machine and trying to do some implicit
> solvent (mm_pbsa/mm_gbsa) calculations. I went through the mm_pbsa.pl
> file and found that SURFTEN has value
> of 1.0 in the input for sander. This is vastly different from the
> 0.005 default value that is shown in the amber 7 user's manual. I'm
> not sure if this is related to interfacing with delphi or not, but I'd
> like to understand the reason for this discrepancy. Any ideas?

The SURFTEN contribution is set to 1.0 in this case just to report the
SAS area. In the mm_pbsa script, the appropriate surface tension and
offset parameters (gamma and beta) are then used to determine the
nonpolar contribution to the solvation free energy, according to which
continuum solvent model is applied (see the mm_pbsa.in file and default
values given at the beginning of
$AMBERHOME/src/mm_pbsa/mm_pbsa_statistics.pm).

Best regards

Holger

>
> Thanks in advance;
>
> Sergio
>
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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla, CA 92037   USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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