[gmx-users] fatal error occuring.

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 18 16:20:37 CET 2011

ibi2010004 at iiita.ac.in wrote:
> Hello Justin,
> After setting up grompp command,i am getting an error "Atoms in the .top
> are not numbered consecutively from 1 (rather, atomnr = 1, while at->nr =
> 1179)".I am heading up step by step taking your aid.
> What should i do?How to correct it??

Without seeing the topology, it is hard to say exactly what the problem is, but 
the [atoms] section of each [moleculetype] must be (as the error says), numbered 
consecutively, starting with 1.  In at least one instance, these criteria have 
not been met.  Note that in the topology, atom numbering is unique to each 
[moleculetype] - that is, the atom numbering in the .gro has no bearing on the 
numbering in the .top.



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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