AMBER Archive (2009)

Subject: [AMBER] molsurf and probe radius

From: David Watson (dewatson_at_olemiss.edu)
Date: Sat May 09 2009 - 12:32:43 CDT

I am trying to evaluate the surface area of a protein-protein complex,
along with the individual protein surfaces areas with mm_pbsa.
When it comes to the probe radius, I would like to represent the
solvent with a radius of 1.9, to reflect methane, in lieu of the
defaults.
I am using bondi radii in my prmtop, and molsurf already accounts for
this in some manner.

In the @MS block, when I try to set the radius to 0.5, which I assume
is added to the default (1.4) bondi radii, I get a large increase in
surface area which does not make sense.
If, instead, I try to set the probe radius to 1.9, I end up with
errors in the mm_pbsa output that look like this:
     Use of uninitialized value in multiplication (*) at /usr/local/
amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1475.

Suggestions, anyone?

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