[gmx-users] Question regarding error

Justin Lemkul jalemkul at vt.edu
Thu Nov 10 16:49:00 CET 2016

On 11/10/16 2:32 AM, Marko Sever wrote:
> Why would such a command:
> gmx pdb2gmx -f system.pdb -i /home/bla/charmm36chol_psm_dopc.ff/PSM.itp -o systemprocessed.gro -water tip3p -ignh -ff charmm36chol_psm_dopc
> give me the following error:
> Fatal error:
> Residue 'PSM' 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
> If I pointed it to the PSM.itp file?

The -i option is output (check the help information), and pdb2gmx does not read 
.itp/.top files at all.

> What is the procedure to manually add the includes into the .top and yet generate the .gro file of the system? Is there any alternative to pdb2gmx or should I use that...
> I got .itp files for the system from Charmm GUI.

If you already got topology files from CHARMM-GUI, why are you running pdb2gmx? 
CHARMM-GUI has done the work for you, and should have provided you with complete 
GROMACS-compatible coordinate, topology, and .mdp files.



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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