AMBER Archive (2007)

Subject: AMBER: ff02 + POL3 - polar interactions !!

From: Pradipta Bandyopadhyay (pradipta_at_iitg.ernet.in)
Date: Wed Apr 18 2007 - 11:04:22 CDT

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?

thanks,

 Pradipta

Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati
Phone: 91-361-258-2213 (office)
e-mail: pradipta_at_iitg.ernet.in
web: http://202.141.80.5/~pradipta/Pradipta.htm

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