GROMACS version:
GROMACS modification: No
Dear Gromacs users,
I’m a new Gromacs user and I’m going to run an energy minimization simulation for a heptamer including a linker (6-aminohexanoic acid) using Charmm36-jul2022.ff. I already created the .str, .itp, and .prm files for the linker, as it is described in the protein-ligand tutorial. The linker has been added to the aminoacids.rtp and residuetypes.dat (as Protein) files.
My question is do I need to modify ffbonded.itp and ffnonbonded.itp files? My impression is that there is no need to do that because the bond types in this linker are already defined in those files.
My second question is do I need to add the .itp file to any other file, for example, the way the ligand was added to the protein topology.top file in the protein-ligand tutorial? If so, to which file(s)?
The last question is do I need to worry about the angle and dihedral angles of the linker? Do I need to define them in other files?
Thanks in advance