[gmx-users] protein-protein complex gets "separated" in EM step

[Gregor Hagelüken]

Dear all,

I am attempting to do a MD simulation off a protein-protein complex. I have successfully performed MD runs on the individual proteins.
Now, I have taken the complex structure (X-ray structure) and ran it through pdb2gmx to get a topology. This also worked. The program does not complain and the complex structure in the resulting .gro file looks just like the input .pdb file in PyMOL.

Next, I performed an energy minimization using these commands:

grompp -v -f minim.mdp -c protein.gro -p protein.top -o protein-EM-vacuum.tpr
mdrun -v -deffnm protein-EM-vacuum -c protein-EM-vacuum.gro

This runs fine, but I noticed that in the resulting protein-EM-vacuum.gro file, the two components of my complex (chains A and B) are separated by ~50 Å. Even if I only run the minimisation for 5 steps.
Any idea why this happens?

Thank you very much for your help!
Cheers,
Gregor



P.S.: I took the minim.mdp file from this website: http://cgmartini.nl/%7Emdcourse/md.html <http://cgmartini.nl/~mdcourse/md.html>