[gmx-users] Fatal error: Atom CG is used in the topology database...

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 23 22:39:38 CET 2012

Andy Somogyi wrote:
> Hi All,
> I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl
> using 
> pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
> I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
> Fatal error:
> Atom CG is used in the topology database, but an atom of that
> name was not found in residue number 1.
> I have not have much luck finding this error in any mailing list.

I've never seen that error before, but it sounds like there is an atom named 
'CG' in the .rtp entry but not in the coordinate file.  Either the atom is named 
differently or it is missing.

> If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen?

No.  The contents of the input coordinate file must match what is expected by 
the .rtp file.  If you have missing atoms, they must be modeled in using 
external software.



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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