getting different dihedral energy with two identical backbones

From: Joyce Yang (
Date: Wed Sep 24 2014 - 16:45:52 CDT


I used the pairinteractionself function to calculated energy of the
backbones of two structures (one is obtained from mutating a single residue
with vmd plugin), respectively. The settings are as below,

"pairInteraction on
pairInteractionGroup1 1
pairInteractionFile namd-temp.pdb
pairInteractionSelf on
coordinates namd-temp.pdb
The beta-coupling column of backbone atoms are set to 1 in the pdb files.

Surprisingly, the calculated dihedral angle energy of the backbones are
different in over 100 kcal/mol between the two structures. It doesn't
really make any sense to me since the two backbones are identical (RMSD=0).

Anyone has an explanation for this?


Joyce yang

Department of Chemistry
University of Alabama at Birmingham

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