[AMBER] Ligand moving out of active site after 250ns

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Sat, 13 Mar 2021 11:38:23 +0530

Dear all,

We are working on a protein - ligand system wherein we ran a production for
500ns. The trajectory seems fine for the first 200ns but then the ligand
moves out of the active site. We assumed it is some issue with the
particular ligand we are dealing with and proceeded on to the second
ligand. But the problem is repeating in the second ligand as well. We
explored the possibility of imaging problem but it does not seem like any
imaging problem. I am attaching our inputs here. If anyone could guide us
regarding a way around this, it would be really helpful.

Sruthi Sudhakar

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Received on Fri Mar 12 2021 - 22:30:02 PST
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