Hi Carlos,
Thank you for your answer. There shouldn't be big differences in protein structure between the
initial and final states because to get the final state I just repositioned the drug at a different position
on the protein from where it is in the initial state and ran a few hundred steps of minimization with a
restraint on much of the system. I think my problem is that unfornutately the elastic forces are
causing Van Der Waals overlap between the images.
Holly
> Holly,
> 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.
> Carlos
>
> On 10/9/07, Holly Freedman <freedman.phys.ualberta.ca> 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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Department of Physics, University of Alberta
Edmonton CANADA
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Received on Wed Oct 10 2007 - 06:07:58 PDT
