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

Justin Lemkul jalemkul at vt.edu
Wed Mar 1 13:58:08 CET 2017

On 3/1/17 7:29 AM, Acqualine Lobo wrote:
> Hello,
> I am trying to simulate a hemoglobin molecule in complex with CO. However,
> pdb2gmx throws a fatal error saying
> Fatal error:
> Residue 'CMO' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I did look up the documentation on errors and as mentioned there it means
> that the residue CMO isn't found in my topology database. However the atom
> types for Carbon Monoxide (CMO as defined in the pdb file) are present in
> many force fields. I changed the name of the residue accordingly but got
> the same error for all the force fields I tried applying (This I also did
> try by separating the ligand and the protein i.e. CO and Hemoglobin
> respectively ). I also tried building the topology using ATB.
> Another, thing I came across in many papers is about modelling CO using the
> 'Straub Karplus model of CO' before simulation. I don't really understand
> how to do that.
> The pdb id of my protein of interest is 1ECO and I'm using gromacs 5.0.7
> I'm an amateur and would be grateful for any help that comes my way. Thanks
> in advance!

Our CHARMM36 port (http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) has 
all the parameters for the Straub-Karplus model as they have been in CHARMM for 
quite some time.

You will need to add a line in specbond.dat (see the manual) to include the case 
of a Fe-C bond and then pdb2gmx should do all the rest.  Note, however, that 
pdb2gmx generates all possible angles and dihedrals, which is not correct 
behavior in the case of ligated heme.  When grompp complains about missing 
parameters, comment out the offending lines (if and only if they correspond to 
angles and dihedrals involving the heme Fe atom).



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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