Yes, it worked. Thank you very much for your information.
Regards,
Nadia
On Mon, Sep 8, 2014 at 12:28 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
> > _______________________________________________
> > AMBER mailing list
> > 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 Wed Sep 10 2014 - 13:30:02 PDT
