[gmx-users] Fatal error: Bond atom type names can't be single digits

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 17 20:41:44 CEST 2012

Sangita Kachhap wrote:
> Hello all
> I am new for gromacs. I have to do MD simulation of membrane protein docked with
> organic molecule.
> I have gerated top and itp for ligand using PRODRG server also generated top
> file for complex.

Hopefully you're not relying on an unrefined PRODRG topology.  See the article 
linked from:


> But when I am generating .tpr file for a POPC system using grompp getting an error:
> creating statusfile for 1 node...
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Cleaning up temporary file gromppWQnjOb
> Fatal error: Bond atom type names can't be single digits.
> I am using gromacs-4.5.5
> Can someone help me to find out where is actually problem is occuring?

It would help to see the topology, but based on a guess I would say that the 
error is pretty explicit that you have atom types that are not appropriately 
named; they are digits.  Atom types can utilize numbers, but only as a part of 
the name.  For instance, "CH3" is a valid atom type, but "3" is not.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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