I’m trying to embed a GPCR-ligand complex 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 maybe I need to use a bigger bi-layer.
Please, any advise will be very appreciated.
Yes, I've followed that tutorial, except that I've used g_membed (which indeed is now part of mdrun) instead of the InfateGRO script. Well, of course there are overlaps because the input file required in both cases is a .gro file with the protein aligned and superimposed with respect to the equilibrated membrane and g_membed or InflateGRO are suppose to remove the overlapping lipids.
For what it's worth, I have never once gotten g_membed to work. The algorithm seems very useful, but after banging my head against my desk over several systems, I gave up altogether and have never used any method other than InflateGRO. Just my $0.02, but given the number of problem reports on gmx-users about g_membed, I suspect there are widespread problems with getting it to work.
You can also follow this simple technique:
http://pubs.acs.org/doi/abs/10.1021/ct500046e
(actually the example in the paper is a very close match to your case)
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