[gmx-users] Error in pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 6 19:35:20 CET 2009

Robert Kretschmer wrote:
> Dear all,
> i have a problem while running pdb2gmx. I want to run a md simulation 
> with HIV-ReverseTranscriptase (PDB: 1TVR & 1HNV). But in pdb2gmx i get 
> the following error:
> "Fatal error:
> Incomplete ring in HIS221"
> I checked HIS221 and found, that it should be an alanine.

The .pdb file probably has the name HIS, but some of the atoms are missing.  If 
it is indeed supposed to be an alanine, change the residue name in the .pdb 
file.  If it is supposed to be HIS, however, then you need to re-build the 
residue using some kind of modeling software.

> What kann I do?

Check for "MISSING" comments in the header of the .pdb file to be sure of what 
you are doing.


> kind regards
> robert
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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