Gas phase minimization

From: Purushottam Dixit (dixitpd_at_gmail.com)
Date: Fri Jun 15 2007 - 16:58:44 CDT

Hi,

I want to put a membrane protein inside a lipid bilayer. Since the
original pdb file has missing residues, I am building residues and
performing a vacuum minimization on the membrane. During the
minimization, the tetrahedral geometries of various amino acids
(especially Arg) get affected to the point that they become
non-sensical.

Is this because I am performing gas phase minimization of a membrane
protein or is it something else?

Regards
Purushottam

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:21 CST