From: Jason Swails <>
Date: Thu, 22 Jan 2015 06:38:57 -0500

> On Jan 22, 2015, at 2:20 AM, Sourav Purohit <> wrote:
> Hi All,
> I am running a simulation on a system consisting of a gold cluster attached
> with a Guanine through a thiol linker. I used xleap to connect the
> different units. During minimization I got an error : " *Bad Topology File:
> Sum of atoms per molecule does not equal NATOM"*. I modifies the topology
> file using (setMolecules command). After the modification,
> minimization worked fine. But during heating using PMEMD, I got the
> error :"*PMEMD
> DOES NOT SUPPORT INTERMOLECULAR PRFs"*. What could be the reason for this.

This error message suggests to me your system has at least one residue that contains multiple molecules (i.e. -- in pmemd, all atoms within a single residue must be part of the same physical molecule). If this is not the case, assumptions that pmemd has made in its parallel algorithm break.

If you send me the topology file and coordinate file off-list, I will try to take a look and see if I can figure out what’s wrong.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 22 2015 - 04:00:02 PST
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