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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--
-------------------------
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)
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Received on Mon Sep 08 2014 - 12:30:04 PDT
