Re: [AMBER] MMPBSA huge VDW values

From: Jason Swails <>
Date: Thu, 12 Jun 2014 07:11:39 -0400

On Thu, Jun 12, 2014 at 3:28 AM, maryam azimzadehirani <> wrote:

> Dear Amber users,
> I am calculation binding energy using on AMBER 12, I tried three
> times and chose different number of frames of my trajectory. In the output
> file I always get huge values for my VDW contribution. In my system I have
> some attached glycans near to the binding site, but not directly in the
> bonding site, I am taking them into calculations as well, but I don’t think
> that may be the reason for huge VDW values since I have the similar out
> values even in the absence of sugars.
> I copied the out put file here. Will be very grateful if you guide me with
> the possible solutions,

​The only way vdW energies can be high is if two atoms get close to one
another. This does not necessarily indicate a problem, as other terms can
compensate. Try visualizing the system and see if anything looks strange
(check the trajectories generated by

The checkoverlaps command​ in cpptraj can help locate close contacts if
they exist.

The major problem I see is the nonpolar solvation term computed in the PB
part. I suggest using inp=1 instead of inp=2 (the default).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jun 12 2014 - 04:30:02 PDT
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