[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 18 15:10:58 CET 2011

ibi2010004 at iiita.ac.in wrote:
> Hello,
> I got all confused.So i started with the beginnning.i generated topology
> for my protein Streptavidin and generated topology for my ligand using
> prodrg2.5 server.
> I am getting error at step editconf i.e.Fatal error:Something is wrong in
> the coordinate formatting of file conf.gro.
> Any suggestions??I made necessary changes to topol.top and conf.gro to
> merge ligand topology.

Something you did was wrong, but it's hard to say.  The problem is with the 
coordinate file, so when you merged the protein and ligand, you broke the format 
somehow.  There are many potential problems.  Please work through the 
protein-ligand tutorial for a guide on how to properly deal with such systems.




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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