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.iitg.ernet.in
web: http://202.141.80.5/~pradipta/Pradipta.htm
-----------------------------------------------------------------------------------
This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated.
http://www.iitg.ernet.in
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 22 2007 - 06:07:14 PDT
