GROMACS modification: No
Dear community members, I am simulating a protein-ligand complex using Gromacs 5.1.4. I am using the latest charmm36 forcefield. Specifically, I am following the protein-ligand complex tutorial by Dr. Lemkul (Protein-Ligand Complex). My ligand happens to be a cholesterol molecule which has an OH group. The ligand retains its original docked pose until the Energy Minimization step. As mentioned in the tutorial, after the minimization step I am restraining the ligand by creating an index file that contains only the non-hydrogen atoms of the ligand. Now after restraining the ligand I successfully performed the NVT equilibration. Surprisingly, when I checked the structure of the protein-ligand complex after NVT step using the nvt.gro file I found that the position of the H atom of the OH group of cholesterol (ligand) was slightly changed as compared to my initial starting structure. I am thinking that this could be due to the fact that I have only defined position restraints on the heavy atoms of cholesterol and as a result of this the position of H atom of the OH group got changed. I would like to have the starting structure of my simulation as close as possible to the initial pdb structure and this is clearly not the case here. My question is that will it be fine if I restrain all the heavy atoms of the ligand along with all the hydrogens. Or is there a way to restrain this particular H atom of the OH group along with the all the other heavy atoms of the ligand. Is there any other way appropriate to deal with this kind of problem? Kindly give your valuable suggestions. Thanks in advance.