[gmx-users] Atoms in the .top are not numbered consecutively from 1

Justin Lemkul jalemkul at vt.edu
Thu Nov 15 15:54:08 CET 2012

On 11/15/12 9:49 AM, Rajiv Gandhi wrote:
> Hello gmx users,
> I have created the topology file for my ligand through PRODRG, protein from
> pdb2gmx. when i try to energy minimize the protein with ligand system it
> gives error that
> Atoms in the .top are not numbered consecutively from 1.
> Could you please tell how can i avoid this error? Thanks...

Number the topology consecutively from 1, as the error states.  You've got some 
topology (maybe something #included in the system .top) that doesn't start from 
1 and must.  Also note that PRODRG topologies are poor quality and need 
significant refinement before they should be used.



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


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