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

Acqualine Lobo acqualobo02593 at gmail.com
Wed Mar 1 13:29:51 CET 2017


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!

- Acqualine Lobo

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