AMBER Archive (2003)

Subject: Misaligned Coords from Alanine Scanning

From: Robert J. Woods (rwoods_at_ccrc.uga.edu)
Date: Fri Feb 07 2003 - 09:54:07 CST

Hi,

We are trying to replace a lysine with an alanine. When we run AS, the
analine coordinates in the resulting snapshots are incorrect. We are using
the parmtop file for the lysine-containing (wild type) protein, which
correctly generates the snapshots for the wildtype, but as I say with AS it
appears to be aligning the alanine incorrectly.

I'm using the atom numbers from the wildtype protein as the pointers for the
CG, CB and C atoms in the lysine.

Any help would be much appreciated.

Robert J. Woods, Ph.D.

Associate Professor of Biochemistry Voice: (706) 542-4454
 and Molecular Biology FAX: (706) 542-4412

University of Georgia http://glycam.ccrc.uga.edu
Complex Carbohydrate Research Center
220 Riverbend Road "One small step for Man,
Athens, GA 30602 one giant leap for Man-9"