[gmx-users] Atoms in the .top are not numbered consecutively from 1
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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