I am trying to perform MD simulations using CHARMM27 force field via GROMACS 2021.4.
The input structure file is a .pdb built from sequence using AmberTools20+tleap. The structure is c-terminated with NH2 and, by default, the "amino acid" is named as NHE (see last 5 lines of .pdb below).
When I attempt to generate GROMACS-required files for simulation, "NHE" residue is not found in the CHARM22 force field residue database.
What is the appropriated residue name for amide in CHARMM?
I tried changing residue name to "NH2", the obvious answer, and got no results. I checked the aminoacids* files, and found no solution.
There might be a simple answer I am missing or not understanding. Please let me know if there is a solution.
""""
ATOM 138 N NHE 11 24.340 34.120 25.340 1.00 0.00
ATOM 139 H1 NHE 11 24.450 34.930 25.930 1.00 0.00
ATOM 140 H2 NHE 11 23.460 33.920 24.870 1.00 0.00
TER
ENDMDL
""""