GROMACS version: 2023.2
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I have done an MD simulation for a protein-dppc bilayer system. After 1000ns I have now achieved a converged system. After 1000ns, the protein is in a corner in the xy plane of the membrane. Now, I want to center the protein. I hope to run md simulation after docking with the docked ligand using this same sytem. Is it correct? Also, I though it is better if the protein is in the center at the begining of my post docking mdruns.
I used gmx trjconv to center the protein giving the final frame of the mdrun (in PDB) as the input structure (as -f ) . However, I could not get a protein-centered system. Could you please tell me a method to do this?
There are a few options; if your protein is multimeric, it’s often preferable to define a single central-enough atom group in the .ndx to use with gmx trjconv -center so that PBC issues don’t come into play. Some more basic solutions involve moving the whole system around with VMD, or using gmx editconf with the -translate option.
If you want to keep your lipids wrapped around the molecule at the end, don’t forget to run gmx trjconv -pbc mol or -pbc res with the final structure.
Thank you so much for your reply!
I tried gmx trjconv in several ways. I tried to center just one chain also. It was also failed. I did not try gmx editconf yet. I will try those ways you have given!
Finally, I could translate the coordinates and get the protein into the center by using this kind of command,
gmx trjconv -f 1000ns.pdb -n onegroup.ndx -o centered.pdb -s 1000ns.tpr -trans 7 1 0 -pbc mol -ur compact
I changed vector values in the -trans flag and checked whether the protein is centered. Finally, I could do it.