AMBER Archive (2009)

Subject: Re: [AMBER] molsurf and probe radius

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon May 11 2009 - 10:03:10 CDT

On Sat, May 09, 2009, David Watson wrote:

> 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,

This is not what is done in mm_pbsa. Look at the generate_pqr() routine in
mm_pbsa_calceneent.pm, or just examine the actual pqr file and radius when
you run molsurf by hand. If you want the solvent-accessible surface for a
probe radius other than 1.4, you will have to change how the pqr file is
constructed. Be sure you understand the distinction between molecular surface
and solvent-accessible surface. (For the latter, the probe radius will be
zero.)

...good luck...dac

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