AMBER: ff02 + POL3 - polar interactions !!

From: Pradipta Bandyopadhyay <>
Date: Wed, 18 Apr 2007 21:34:22 +0530 (IST)

Dear All,

 I have done MD simulations using AMBER8 with both ff99 + TIP3P and ff02 +
POL3 for my protein. Two trajectories were run for each force field.
Always I am seeing that some polar interactions (and also some H-bonds)
are slightly stronger for ff02 + POL3 - the average distance between the
atoms involved in the polar interaction (and in H-bond) is slightly
shorter for ff02 + POL3.

Has anyone found the same? Is it possible to explain?



Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati
Phone: 91-361-258-2213 (office)

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Received on Sun Apr 22 2007 - 06:07:14 PDT
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