Hi David,
Thanks for reminding me!
I used iwrap=1, and also used autoimage to try to image the ligand. But it
still stays out of the pocket.
I convert ligand 1 to another ligand 2 which has a similar structure to
ligand 1.
Best,
Fanyu
On Sat, Oct 15, 2022 at 8:28 PM David A Case <david.case.rutgers.edu> wrote:
> On Sat, Oct 15, 2022, Fanyu Zhao wrote:
> >Hi David,
>
> Please send amber-related questions to the mail reflector,
> amber.ambermd.org,
> and not to me personally. That way, many people can see your question and
> try
> to help, and the answers can help others with similar questions. See
>
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> >
> >I actually visualised trajectories for every window. But the input files
> >for the window with separation and the one working find are basically the
> >same, except the value of clambda. The ligand just suddenly popped out
> from
> >the pocket during production run with GPU.
> >
>
> How finely are you sampling snapshots in the trajectory. If the ligand
> "suddenly popped out", it might indeed be an imaging problem. Are you
> running with iwrap=0?
>
> At the endpoints of some TI runs, the ligands become decoupled from the
> environment. Are you converting one ligand to another, or converting the
> ligand to "nothing"?
>
> ....dac
>
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Received on Sat Oct 15 2022 - 21:00:02 PDT
