Re: [AMBER] mm-pbsa & extra-point

From: Jason Swails <>
Date: Thu, 5 Mar 2015 17:38:29 -0500

On Thu, Mar 5, 2015 at 4:42 PM, Emilio Angelina <> wrote:

> Dear Amber users/developers:
> I ran MD simulations of protein-ligand complexes where the ligand has an
> extra-point on an halogen atom to simulate the sigma hole. I did not have
> problems to get the MD trajectories (actually I had faced a lot of issues
> but I could solve it thank to your help).
> Now I want to compute the complex free energy with the script
> but it gives me very large values of the Van der Walls components. Is It
> due to the extra-point? Could this have something to do with the fact that
> there is no Van der Walls radius defined for the extra-point ? I have
> pasted below part of the mm-pbsa output (see also the attach) so you can
> see what I mean.

​Extra points do not work with the GB code, but it should have given you an
error (rather than running). I wonder if NAB doesn't have this check (or
if it actually supports EPs...)

That said, these numbers seem to be more caused by inconsistencies between
the generated trajectories and the complex/receptor/ligand topology files.
I would suggest visualizing these trajectories (_MMPBSA_complex.mdcrd.0,
_MMPBSA_receptor.mdcrd.0, etc.) to see if they appear warped. If so, you
need to double-check that you don't have any extra waters or anything in
the complex or receptor topology files, and make sure that the topology
files map correctly onto the trajectory files that are generated.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 05 2015 - 15:00:02 PST
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