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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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