Residue 44 named DC of a molecule in the input file was mapped to an entry in the topology database,

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am trying to perform energy minimization for my ssdna structure using CHARMM36 all-atom force field in gromacs.
gmx pdb2gmx -f bbbbddD.pdb -o process.gro -ter -ignh then I select 1: CHARMM36 all-atom force field (July 2020)
and
I selected water model 5 SPC/E
then I am getting this error Fatal error:
Residue 44 named DC of a molecule in the input file was mapped
to an entry in the topology database, but the atom O5’ used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
How to fix this error ?

2

Hi,

“Residue 44 named DC of a molecule in the input file was mapped
to an entry in the topology database, but the atom O5’ used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.”

I suggest to check that atom/residue names in your pdb match the
one of the force field rtp file

Just a general comment, CHARMM force field is parameterized in line with TIP3P water model and not SPC/E.

Best regards
Alessandra