From: Jason Swails <>
Date: Mon, 25 Jul 2016 11:10:08 -0400

On Thu, Jul 21, 2016 at 6:30 AM, Anna Cebrian Prats <>

> Good morning
> I have used cpptraj to check the topology and the coordinates looks a like
> in a pdb
> and at the beginning of the process with this command : cpptraj
> I have obtained this error. What does it means? My topology is created
> wrong?
> How can I solved? I already check in the manual and with a tutorial and
> suggest that the problem is with the atom order. However, I have been
> renumbered by the pdb4amber. Also can be that the bond is not defined but
> the frcmod file contains such information

‚ÄčThis is a well-known bug in tleap that does not result in the correct atom
ordering for systems with cross-linked molecules in some instances.

You can use the "fixatomorder" command in cpptraj to fix your topology file
and trajectory files.


Jason M. Swails
AMBER mailing list
Received on Mon Jul 25 2016 - 08:30:03 PDT
Custom Search