GROMACS modification: No
Sorry for my poor English.
Please lend me your help, everyone.
I have three questions for you.
①I would like to use the “AMBER” force field to flow the structure of the covalent linkage between sugar and protein with “GROMACS”. I’m thinking of using “CHARMM-GUI”, but what are the bonds, angles, and torsions that contain covalently bonded atoms? In other words, is it derived from either ff14SB or GLYCAM-06j?
②Next, I already finished MD and have each output file. what if I want to add 50ns?
③I would like to reproduce the binding of the ligand to the RNA at 1 μs MD, but I think it would be very difficult in a normal setup. Any suggestions on how to do this?