Fanyu,
if your ligand leaves the binding pocket during the simulation, then
this seems an outcome of your simulation experiment, and no artifact due
to wrapping or mirroring effects.
Maybe the perturbation you introduced is too large to allow the ligand
to stay in its initial position?
Although I'm no expert at TI, I'd suggest to simulate the two different
ligand systems (=states) separately to ensure that they both produce
bound ligands.
Regards,
Anselm
Am 17.10.2022 um 15:41 schrieb Fanyu Zhao via AMBER:
> Hi David,
>
> Sorry for the unclear statement.
>
> I tried iwrap=0 once and the result remained the same; the ligand moved out
> from the pocket. More accurately, the ligand is keeping moving during the
> MD process, from the inside of the pocket to the outside. So there is a
> structure with the ligand half-way out of the pocket.
>
> Best,
> Fanyu
>
> On Mon, Oct 17, 2022 at 9:29 PM David A Case <david.case.rutgers.edu> wrote:
>
>> On Sun, Oct 16, 2022, Fanyu Zhao wrote:
>>>
>>> I used iwrap=1, and also used autoimage to try to image the ligand. But it
>>> still stays out of the pocket.
>>
>> Did you try using iwrap=0? We still don't know what the word "suddenly"
>> means in your statement that "the ligand just suddenly popped out from the
>> pocket". Do you ever see a structure where the ligand is half-way out of
>> the pocket?
>>
>> It still seems possible that this is just an imaging problem.
>>
>> ....dac
>>
>>
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Received on Mon Oct 17 2022 - 08:00:02 PDT
