GROMACS version: 2020
I am simulating a protein-ligand complex using charmm36-july22 forcefield based on the GROMACS tutorial Protein-Ligand Complex. The ligand is SAM. For this i have included the contents from toppar_c36_jul22.tgz (source- https://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul22.tgz) and the patch file toppar_all36_prot_na_combined.str
This is the error that I am getting at the pdb2gmx step.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Now there are 6 atoms. Deleted 21 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Program: gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130)
Fatal error:
Residue 1 named SAM of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
The pdb structure of SAM is attached below.
modifiedSAM.txt (2.8 KB)
for your reference.