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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>
>
>
> --
> -------------------------
> 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 - 13:00:02 PDT
