AMBER: neb for path between binding sites

From: Holly Freedman <>
Date: Tue, 9 Oct 2007 15:09:50 -0600

I was wondering if it would be possible to use NEB to find a minimum energy path for a drug between
two close binding sites on a protein in order to determine the energy barrier for motion of the drug
between the two sites? In fact I tried to do this (following the tutorial on the web site) but the energy
became infinite within a few steps of heating the system; also the NEB program didn't seem to separate
the images much. I was using 15 images at each site. I was hoping this method might be helpful for
my problem, but now it seems it may be completely inapplicable. I would appreciate hearing if there is
any way to apply the NEB method to this kind of problem.
Thanks in advance,

Department of Physics, University of Alberta
Edmonton CANADA
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Received on Wed Oct 10 2007 - 06:07:52 PDT
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