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

Spyridon Vicatos svicatos at bioacademy.gr
Thu May 29 14:58:01 CEST 2014

I checked you question. In order to create my membed.tpr file, I used

grompp -c prot_dppc.gro -p *system.top* -f membed.mdp *-o membed.tpr*

None of the files contain water. Not prot_dppc.gro, not the system.top. 
As for membed.mpdb, I am not sure where to look at, to see if there are 
any "waters" option used.


On 27/05/2014 02:59 ??, Justin Lemkul wrote:
> 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 
>> 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 
> -Justin

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