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

Spyridon Vicatos svicatos at bioacademy.gr
Tue May 27 11:39:47 CEST 2014

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 

g_membed -f membed.tpr -p system.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -o 

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 

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.

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