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

[Justin Lemkul]

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

========================================