VMD-L Mailing List

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Mon Feb 07 2005 - 11:26:16 CST

Hi All,
   I downloaded the VMD v1.8.3 beta version to use the SASA command to
measure solvent accesible surface area.

   I can analyze my dcd's with it, BUT I am getting a physically
unreasonable result. The result is that the Surface area of the sidechains
is larger then the Surface area of the protein as a whole!!!

   The SA,protein = SA,sidechains + SA,backbone, should be true. But
instead I find:
   SA,protein < SA,sidechains + SA,backbone

with the SA,sidechains > SA,protein.

   My initial guess is the sasa command is not taking into account the
excluded volume of the backbone when it measures the surface area of the
sidechains, and vice-versa.

   Any suggestions about how to get self-consistent results?

Thanks!
Ed

PS- for srad I use 1.4, is this resonable?