[gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

Justin Lemkul jalemkul at vt.edu
Thu Mar 2 15:21:02 CET 2017

On 3/2/17 9:18 AM, Acqualine Lobo wrote:
> Thanks for the quick reply Dr. Justin!
> I did follow what you mentioned, however I still get the same error. I also
> tried changing the residue name in the pdb file to match the atom type as
> in the .atp file, the error still remains only with a different residue
> name. Instead of "Residue 'CMO' not found in topology database" it says
> "Residue 'CM' not found in topology database".
> This is my first time using gromacs and I feel really lost. Any suggestions
> are welcome.

There is nothing in the .atp file that will help you correct the .pdb file. 
Coordinate files have no type information, only residue and atom names.

The CHARMM36 residue is called "CO" (see the .rtp file, which is what matters) 
and the atoms are named simply C and O.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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