[gmx-users] Error while trying to create a membrane-protein system

Justin Lemkul jalemkul at vt.edu
Tue May 27 14:07:55 CEST 2014

On 5/27/14, 5:32 AM, Spyridon Vicatos wrote:
> Hello all.
> I am a brand new user of Gromacs, and I am not even sure I am sending this email
> to the appropriate people. If my email goes to the wrong people, I apologize in
> advance
> I am trying to create a pdb (or gro) structure which containts protein and
> membrane, DPPC to be exact.
> After following a certain path, I have managed to create all necessary files,
> and now I am about to use command g_membed. So, I use g_membed as follows
> g_membed -f membed.tpr -p system.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -o
> memtraj.trr
> Gromacs gives me a message, saying that it has created a .dat file, and that now
> I need to run mdrun in a specific way.
> So I call mdun as follows
> mdrun -s membed.tpr -membed membed.dat -o memtraj.trr -c membedded.gro -e
> ener.edr -nt 1 -cpt -1 -mp system.top
> Gromacs then interactively asks me to choose "Select a group to embed in the
> membrane:" and I choose "1", protein
> Then it asks me to choose "Select a group to embed Protein into (e.g. the
> membrane):" and I choose "13", DPPC
> After that, it looks like mdrun crushes, and it gives me the following error:
> "-------------------------------------------------------
> Program mdrun, VERSION 4.6.5
> Source code file:
> /home/$$$/PROGRAMS/GROMACS/gromacs-4.6.5/src/gmxlib/mtop_util.c, line: 215
> Software inconsistency error:
> gmx_mtop_atomlookup_settle_init called without settles
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------"
> I have no idea how to address this error. Can someone tell me what my mistake
> may probably be? I kind of found the source code online, but still I am not
> familiar (yet) with the variables.
> If you can forward this email to the appropriate people, I would greatly
> appreciate it.

You're in the right place.

Is there water in the system?  It looks as though the code assumes there will be 
water present (which is the only molecule that uses SETTLE).



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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