GROMACS version:
GROMACS modification: Yes/No
when i give command for topology file, this error is shown
“For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.”
Hi,
I believe this is because the force field you are using does not have an entry for “H3”. You have two options: you either add a new rtp entry for H3, or you use the flag -ignh when running the pdb2gmx command as it is suggested by the error message.
More details are provided here: https://manual.gromacs.org/current/user-guide/run-time-errors.html
After adding –ignh
Fatal error:
Residue 4 named ARG of a molecule in the input file was mapped
to an entry in the topology database, but the atom CD used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.