GROMACS version: 2020.6
GROMACS modification: No
Dear GMX users,
I’d tried to simulate the SARS-COV-2 Spike glycoprotein obtained from CHAMM-GUI into GROMACS using charmm36-feb2021.ff.tgz (obtained from: MacKerell Lab) but on pdb2gmx I faced this error:
[… many lines of information …]
Opening force field file /opt/gromacs-2020.6/share/gromacs/top/charmm36-feb2021.ff/merged.arn
Program: gmx pdb2gmx, version 2020.6
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)
Atom N in residue BGLC 0 was not found in rtp entry BGLC with 24 atoms
while sorting atoms.
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
CHARMM36 defines some building blocks (BGLC, BGLCA, BGLCA0, BGLCN0, BGLCNA) on merged.rtp file and since pdb2gmx reads 3-long residue type characters (columns 18-20) and CHARMM36 presented 5 or 6-long residue name on merged.rtp file, so how can I correct assign these N-glycosilated residues on my protein generating my top files?