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From: Ramin Ekhteiari (ramin_ekh_at_REMOVE_yahoo.com)
Date: Mon Jul 07 2014 - 14:59:42 CDT
I'm trying to calculate pair interaction energy between protein and ligand via NAMD energy plugin. In the active site of the protein near the ligand, there are only 2 or three water molecules were placed, so how should I set the dielectric constant, should it be 1 or more ?
I will appreciate for your answers.