Gas phase minimization

From: Purushottam Dixit (
Date: Fri Jun 15 2007 - 16:58:44 CDT


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

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


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