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

From: Kenneth Huang <>
Date: Sat, 13 Mar 2021 11:43:09 -0500


Someone else might see something off, but I didn't see anything that'd be
responsible other than your slightly higher temperature. But devil's
advocate- 1) are you sure the active site/ligand conformation is actually
correct, or 2) are you sure the ligand isn't just doing what it's supposed
to do, ie leave and rebind?

If you're certain of the above, you could trying putting some distance
constraints between one of the ligand/protein atoms to keep it tethered in



On Sat, Mar 13, 2021 at 1:09 AM Sruthi Sudhakar <> wrote:

> 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.
> Regards,
> Sruthi Sudhakar

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Received on Sat Mar 13 2021 - 09:00:02 PST
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