Re: [AMBER] binding free energy analysis

From: Jason Swails <>
Date: Wed, 08 Jan 2014 12:43:34 -0500

On Thu, 2014-01-09 at 00:55 +0800, Nitin Sharma wrote:
> Respected sir,
> >>I suspect what you are hitting here is a minor issue in tleap when it deals with improper torsions with 2 atoms of the same type.
> Is there anything I can check to negate this error? Or I can ignore this error?

You can ignore this error.

> >> Overall, the DIHED contribution to the binding free energy is negligible (but still has at least one frame larger than the 0.001 kcal/mol cutoff that uses to issue a warning). You should be safe to ignore this warning in this case.
> Which value are you referring to? Also what should be safe zone to ignore such error.

The DIHED contribution to the binding free energy, which should be
exactly zero, is not:

Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of Mean
> > -------------------------------------------------------------------------------
> > BOND -0.0000 0.0001 0.0000
> > ANGLE -0.0000 0.0001 0.0000
> > DIHED -0.0005 0.0079 0.0001

But it is close enough to zero that it can be ignored. So what I called
"negligible" were the differences that gave rise to the warning you saw.
So the warning can be safely ignored in your case.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 08 2014 - 10:00:02 PST
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