[gmx-users] Re: Error in PDB2GMX

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 7 01:10:35 CEST 2009

Please keep all Gromacs-related correspondence on the gmx-users list.  As I have 
said dozens of times, I do not advertise myself as a private tutor, nor do I 
always have the right solutions.

sunny mishra wrote:
> Dear Justin,
> I read your solutions always in the GROMACS discussion topics. I have
> also got one problem this time while using pdb2gmx. 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.

Which CG model are you using?  The one most commonly used with Gromacs is 
MARTINI, and its setup procedure does not require the use of pdb2gmx; the 
authors make scripts available that generate your topology for you.


> 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.
> Thanks,
> Sunny Mishra


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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