Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!

From: Jason Swails <>
Date: Fri, 20 Mar 2015 08:06:49 -0400

On Thu, Mar 19, 2015 at 6:12 PM, Jorgen Simonsen <>

> Ok I know what the problem is but I do not know how to solve it or if can
> be solved using PMEMD.mpi; when I add bonds between my metal ion and
> histidine residues that are coordinating it I get the warning described :
> ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not
> contiguous!

​This error is caused when you use the "bond" command in tleap to link
together non-adjacent molecules. This is a known bug in tleap. There are
two ways to work around it, but both involve fixing the topology file after
tleap writes it out (broken).

ParmEd should tell you something along the lines of "use setMolecules to
fix this". If it doesn't, it's likely because you are using a very old
version of Amber (12 or earlier?). So make sure you're using the latest
version of AmberTools, run the "setMolecules" command in ParmEd, and make
sure you save both a prmtop file and a corresponding restart file that you
can use for simulations.

In my last email I showed a sample parmed input file that will accomplish
this task.


P.S. The fixatomorder command in cpptraj will do the same thing

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Mar 20 2015 - 05:30:06 PDT
Custom Search