Have you visualized it? We would need to know if it dissociated or if it's
a jump. If slowly dissociated, I suggest starting a new email thread with
the relevant subject.
On Sep 8, 2014 3:35 PM, "George Tzotzos" <gtzotzos.me.com> wrote:
> I have encountered a similar problem.
>
> I’ve conducted several 100ns MD simulations on the same small protein
> receptor using different non-polar ligands. The results obtained were quite
> consistent. When I used a ligand with a polar group (de-protonated
> carboxylate moiety) the ligand flies out of the binding pocket after a few
> nanoseconds simulation. There is biological evidence that the ligand binds
> on the receptor.
>
> Any suggestions regarding this behavior would be most welcome.
>
> Regards
>
> George
>
> On Sep 8, 2014, at 4:28 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > As Carlos said, this may be an imaging issue. Try the 'autoimage'
> > command in cpptraj to reimage your trajectory to remove any imaging
> > visual artifacts:
> >
> > parm <topology file>
> > trajin <trajectory>
> > autoimage
> > trajout reimaged.nc
> >
> > Hope this helps,
> >
> > -Dan
> >
> >
> > On Mon, Sep 8, 2014 at 1:03 PM, Nadia Li <amber.nadiali.gmail.com>
> wrote:
> >> Dear amber users,
> >>
> >> I am running a protein-ligand complex, and in my production run, I
> found in
> >> the first 6 ns, the ligand was outside of the binding site, but then it
> was
> >> back in the binding site.The binding site is shallow which may explain
> why
> >> at the beginning the ligand shifted away from the site, but I don't
> >> understand how come it is back to the site later? Could anyone explain
> >> this?
> >> Thanks for your help in advance!
> >>
> >> Regards,
> >> Nadia
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Sep 08 2014 - 13:00:02 PDT
