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