Re: AMBER: neb for path between binding sites

From: Carlos Simmerling <>
Date: Tue, 9 Oct 2007 17:25:27 -0400

it might be hard in the current NEB implementation.
it requires GB solvation, which may or may not
be ok in your system. You should do non-NEB MD first
to make sure that things are stable. It does seem
odd that the energy went up so fast, we haven't seen
that in the limited NEB work I have done. It's not
that efficient for large systems, though, and also will try to
map a path for any differences in the protein structure
between your two states, which you might not want.
We are working to fix that and also support explicit water
for the next version of Amber. For now maybe others with
more experience can take a look at your inputs if you send
them and see why the energy is infinite.

On 10/9/07, Holly Freedman <> wrote:
> Dear AMBER,
> 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,
> Holly
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
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Received on Wed Oct 10 2007 - 06:07:53 PDT
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