VMD-L Mailing List

From: Ramin Ekhteiari (ramin_ekh_at_REMOVE_yahoo.com)
Date: Wed Jun 04 2014 - 12:45:36 CDT

Hi dears, I am trying to calculate energy between one polar amino acid residue (GLU) and a small ligand using NAMD energy plugin during a course of MD trajectories, but I face with results as below,   (the electrostatic energy values are not reasonable for a H-bond). Frame         Time          Elec          VdW           Nonbond       Total         0             0             -105.632      -3.0657       -108.698      -108.698      1             1             -103.383      -3.9904       -107.373      -107.373 Would be grateful for any comments, Cheers, Ramin.