[gmx-users] peptide lipid simulation

Justin Lemkul jalemkul at vt.edu
Thu Sep 24 15:28:52 CEST 2015

Please be sure to keep the discussion on the mailing list.

On 9/24/15 9:24 AM, badamkhatan togoldor wrote:
> Thanks
> Oh, charmm37 is working fine. And now on the grompp give me this error.
> Fatal error:
> No molecules were defined in the system
> For more information and tips for troubleshooting, please check the GROMACS

Did you visit the URL given in this message?  Most common errors have solutions 
listed here.

> Is it depending on my peptide.pdb file, there was several kind of pope.pdb
> files, so i don't know which one is suitable for me! another pope.pdb file gave
> me different error on the pdb2gmx.

I have no idea what this means.  Several coordinate files?

> Fatal error:
> Residue 'POP' not found in residue topology database
> Any advice?

"POP" is not a valid residue name.  See the force field .rtp file for valid 
names (spoiler alert: for POPE, the residue name is POPE).

You may want to use CHARMM-GUI to build this system and write its topology if 
you are not familiar with building complex systems.



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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