Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop

From: Jason Swails <>
Date: Thu, 31 Jul 2014 23:33:05 -0400

On Thu, Jul 31, 2014 at 11:07 PM, Vivek Shankar Bharadwaj <> wrote:

> Hi Jason,
> Some more Info.
> The number of atoms in the (complex) = number of atoms in (receptor +
> ligand) topology files.
> However, I am running a simulation of an enzyme in an ionic liquid water
> mixture. I did consider the IL to be part of the solvent and stripped it
> when getting the complex prmtop.
> Could this have anything to do with the NATOM mismatch?

​Probably. You probably have to change the "strip_mask" variable to strip
the IL residues out of your system if you didn't include them in your
topology file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 31 2014 - 21:00:02 PDT
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