GROMACS version: gromacs-2022.2
When I run the gromacs commands, The topology generation is not happening and the job is getting aborted. Please help me to fix this issue.
I am attaching the pdb file along. I am using the charmm36 forcefield.
file.txt (159.1 KB)
I don’t think anyone will be able to help you without more information. What goes wrong?
The topology file is not being generated.(file.top)
the file is created but it’s empty and thus the further steps cannot run.
command line : gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -p $NAME.top -ignh -water tip3p -ff charmm36-jul2022
Any other information needed, please let me know
I guess you get error messages, right?
yes, i do.
They should say what the problem is. What do they say?
You need to make sure that your atoms are named correctly according to the topology database entries. There doesn’t seem to be a CG2 atom in residue 5 (THR) in your input file.
See if Residue mapped into topology database but atom name not found in file? - #10 by amei or Fatal error: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topol helps.
