[gmx-users] Problem inserting protein into a POPC bilayer

Juan Munoz-Garcia juan.munoz-garcia at bioch.ox.ac.uk
Mon May 26 11:04:17 CEST 2014

Although I don’t think that changes anything, I forgot to say it’s a GPCR-ligand complex what I’m trying to embed into the POPC membrane.

Dear gromacs users,

I’m trying to insert a GPCR protein into a 128-lipid POPC bilayer (popc128a.pdb structure from Peter Tieleman’s group) using the following set of commands with GROMACS 4.6.5 (of course the protein is aligned with respect to the membrane and both protein and membrane merged in merged.gro file)

grompp_mpi -f membed.mdp -c merged.gro -p merged.top -o membed.tpr -maxwarn 10
g_membed_mpi -f membed.tpr -p merged.top -o merged.trr -c merged_membed.gro -e merged.edr -dat merged.dat -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
mdrun_mpi -v -s membed.tpr -membed merged.dat -o merged.trr -c membed_equil.gro -e merged.edr -nt 0 -mp merged.top

As mdp file I’m using the sample.mdp file found here: http://wwwuser.gwdg.de/~ggroenh/membed.html

To avoid job crashing due to too many LINCS warning, I’ve set GMX_MAXCONSTRWARN to -1.

However, I get the following error messages followed by a segmentation fault:

WARNING: Listed nonbonded interaction between particles 6672 and 6675
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

step 0
Step 1  Warning: pressure scaling more than 1%, mu: 3.1066e+25 3.1066e+25 5.37403e+24
./g_membed.in: line 3: 30053 Segmentation fault      (core dumped) mdrun_mpi -v -s membed.tpr -membed merged.dat -o merged.trr -c membed_equil.gro -e merged.edr -nt 0 -mp merged.top

I’m quite lost at this point as I’ve followed the protocol stated in the original paper. One of my thoughts is that the 128-lipid membranes is too small for my GPCR, as it overlaps with most of the lipids in the membrane… so that I maybe need to use a bigger bilayer.

Please, any advise will be very appreciated.

Juan C. Munoz-Garcia

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