GROMACS version:
GROMACS modification: Yes/No
Here post your question
when i start the simulation with the help of gmx pdb2gmx -f -o1.gro -p 1.top -water spce
then select the forcefield i choose the charmm27 all atom and the fatal error coming.
“Residue 443 named SER of a molecule in the input file was mapped
to an entry in the topology database, but the atom OG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.”
You have at least one missing atom (Ser443 Oγ) that needs to be modeled in before the coordinates can be processed by pdb2gmx.
Okay, understood. Thank You so much.