AMBER Archive (2003)

Subject: Re: AMBER: GB/SA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue Nov 11 2003 - 14:47:59 CST

Chris Moth schrieb:

...
> I grepped for surften in the amber7/src/sander/*.f files, and found no
> other use of the variable, so setting it to 1.0 should not harm any other
> calculation.

That's right.

...
> In other words, The surften value that mm_pbsa.pl passes to sander is not
> the same as the SURFTEN value you pass to mm_pbsa.pl. SURFTEN and SURFOFF
> are apparently only used by the mm_pbsa_statistics.pm perl script only
> after the sander calculations with surften=1.0

That is also right. The reason is that in this way one can use one SAS
calculation together with different SURFTEN and SURFOFF values to
determine different G_nonpolar contributions (e.g. if the polar part to
the solvation free energy is determined by GB and solving the PB
equation in one run).

...
> Also, if you prefer to use the molsurf program instead of sander's LCPO
> implementation, molsurf should work stand-alone, but you will have to sort
> through the C code (in mm_pbsa directory) and build an input .pdb file for
> each frame of interest. Typing molsurf gives:
> Usage: molsurf pqrfile probe_rad

Just one comment - setting MS to "1" in the mm_pbsa.in file leads to
using molsurf for calculating the SAS, i.e. conversion of the snapshot
files to pqr files is done within mm_pbsa.pl.

Best regards

Holger 

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++

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