GROMACS version: 2021.5
GROMACS modification: No
I am trying to model a protein that has an N-terminally methylated Phe1 residue (NMFP), but this is not a standard N-terminal patch in the CHARMM-GUI. I was able to parameterize N-Methyl-Phe in CGenFF and add the modified residue to the protein structure using Pymol (replacing the Phe1 residue and creating a new bond between NMFP and residue Thr2). Where I am running into difficulties is getting the engineered residue recognized in the CHARMM-GUI workflow, specifically not having that residue disappear in the pdbreader output of step 1. I’m not sure how to take the info in the .str file from CGenFF and incorporate that into the proper topology and parameter files requested in the PDB reader steps. I haven’t been able to find a good tutorial on incorporating modified residues through CHARMM-GUI, so maybe there is a different, command line approach. Any insights, suggestions, and tips would be greatly appreciated