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 - 07:00:03 PDT
