From: Holger Gohlke <>
Date: Tue, 11 Nov 2003 21:47:59 +0100

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 passes to sander is not
> the same as the SURFTEN value you pass to SURFTEN and SURFOFF
> are apparently only used by the 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 file leads to
using molsurf for calculating the SAS, i.e. conversion of the snapshot
files to pqr files is done within

Best regards


Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Tel.:  (+49) 69-798-29503; Fax: (+49) 69-798-29826
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Nov 11 2003 - 20:53:01 PST
Custom Search