GROMACS version:2020
GROMACS modification: Yes
I have a small peptide, which I want to simulate in gromacs using CHARMM-2020 forcefield. My peptide consist of 4 residues, viz. Ala-Val-Ala-Trp. A tert-Butyloxycarbonyl protecting group is present in the N-terminal position of Alanine. Can anyone help me, that how I can properly generate topology for such kind of modified amino acid residue, and how to add them in gromacs forcefield? I have read the gromacs manual, and followed this link, " http://manual.gromacs.org/current/how-to/topology.html#adding-a-new-residue ". I tried to generate the topology from CgenFF and the atom name and bond information into the .rtp file, I have no information about .hdb update. But still i am ubable to solve this problem, only getting error n error. Can anyone help me regarding this problem, with some example files.
Thank you in advance.
You should not try to merge something from CGenFF into a constituent residue of a polypeptide; it will not be sufficiently accurate. Atom types and bonded parameters exist in the CHARMM force field for esters and the alkyl group you need, but you would need to properly parametrize charges and some dihedrals. You should look at http://ffparam.umaryland.edu/ to do this, as it will require QM calculations and some parameter fitting.