you probably need to perform imaging on your trajectory. search the
archives for "imaging dimer" to get some suggestions.
On Mon, Sep 8, 2014 at 3:03 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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Received on Mon Sep 08 2014 - 12:30:02 PDT
