[gmx-users] Error in PDB2GMX

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 7 01:27:26 CEST 2009

sunny mishra wrote:
> Hi,
> I am working on HIV-1 Protease with PDB ID 1A8G.pdb. I am trying to convert this
> protein structure to COARSE GRAINED protein structure and I am done
> with that but when I am trying to make the topology and conf.gro file
> from my CG structure of 1A8G.pdb using pdb2gmx it gives me the FATAL
> ERROR something like this.
> FATAL ERROR : Incomplete Ring in HIS 69.
> Now, I am really confused that what will be the solution of this
> thing. I am also new to GROMACS and I have no idea about the solution
> of this problem. I would highly appreciate your help for the same.

Visit the MARTINI site.  They have scripts that generate CG protein topologies. 
For MARTINI, pdb2gmx is not necessary.


> Thanks,
> Sunny Mishra
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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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