Re: jarrod

From: Holger Gohlke <>
Date: Thu, 12 Jun 2003 08:18:43 -0700

Jarrod Wesley Barnes wrote:
> I was curious to know if one could calculate the solvent
> acessible surface area for an atom or residue in a trajectory
> file over the course of a MD simulation in one of the programs
> associated with Amber. If not, is there a program that is
> capable of doing this calculation over the course of the
> trajectory ?

Within the mm_pbsa module, at least residue based (+
side-chain/backbone) decomposition is possible. For that, you need to
break down your trajectory into single snapshots, however.
Have a look at the .DECOMP section in the file. You also need
to choose GBSA=2 in the .GB section and to set SURFTEN=1.0 . This will
give you the SAS in the results file (in the column where otherwise the
nonpolar contribution to solvation free energy is reported). Please
note, with GBSA=2, SAS is computed here as sum over (non-buried)
surfaces of (approximated) spheres.

Best regards


> thanks,
> Jarrod Barnes
> Grad Student at UGA BIOCHEM
> PI: Dr. Rob Woods

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
Received on Thu Jun 12 2003 - 16:53:01 PDT
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