[gmx-users] pdb2gmx error

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 2 02:21:22 CEST 2012

Acoot Brett wrote:
> Dear All,
> I just run a pdb2gmx of a protein, the error message is "
> Fatal error:
> Atom CG is used in an interaction of type atom in the topology
> database, but an atom of that name was not found in residue
> number 5."
> According to the sugestion I have tried to find the reason in "
> http://www.gromacs.org/Documentation/Errors"
> But in that part of Document no this error was explained.

It means that there is an atom named "CG" in the .rtp entry for whatever residue 
5 is, but your coordinate file has no such atom.  Either you have a naming 
mismatch or a missing atom.


> I am looking forward to getting an explaination from you.
> Cheers,
> Acoot


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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