AMBER Archive (2004)

Subject: AMBER: restraining internal coordinates

From: Taner E. Dirama (
Date: Thu Sep 16 2004 - 11:53:51 CDT

Dear all,
I would like to simulate a protein cluster consisting of 4 protein molecules in
a solvent. I want to let the center of masses of the proteins move while to
keep the internal coordinates of the proteins fixed (or restrained).
ibelly and ntr options impose cartesion coordinate restraints which will keep
the center of masses restrained as well. Torsional angle restraints in nmr
options, as far as I understood from the manual, allows one to define the
ranges of torsional angle values for specified dihedrals. However, same
dihedral angles in the same type of residues in a protein may have
significantly different dihedral angles. Therefore, the range specified would
allow the proteins to deviate from their initial (crystalline) structures.

Is there a way that can do this?


Taner E. Dirama
Department of Polymer Science 
The University of Akron
Akron, OH
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