Re: [AMBER] AMBER20 TI calculations

From: Adrian Roitberg <>
Date: Fri, 27 Nov 2020 12:21:09 -0500

Hard to tell without more details, but...

You are getting warning about NMR restraints, I would check those first.

What happens if you take the restraints out just to check on the run ?

Your box size seems to be immense. I very much doubt that your system is
91 MICROMETERS to the side !


On 11/27/20 12:15 PM, Debarati DasGupta wrote:
> [External Email]
> Hello everyone,
> I am running an absolute binding free energy calculation on a ABL kinase system ( ligand is isopropanol), I have applied distance based restraints to keep the ligand in the pocket:
> However, after minimization, the system gets unstable in the temperature ramping simulation I get this: ( see picture below). Any ideas/thoughts on how to prevent this?
> I have used softcore potentials and I am doing a stepwise de-charge, then disappearing the LJ interactions.
> Thanks
> Debarati
> [cid:image001.png.01D6C4B6.D8F0CCC0]
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Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
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Received on Fri Nov 27 2020 - 09:30:02 PST
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