Urgent help: atom and/or residue naming needs to be fixed

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question:

Residue 14 named NME of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

As forcefield I used AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) and TIP3P as water model.

How can I fix this error?
Thank you

2

GROMACS will have a list of atoms provided by the forcefield that it expects to find in a given residue. It seems an NME residue in your input file is missing a carbon atom. You may need to check whether there is some issue with labeling in the input file, but you’ll likely have to find a new input file with all the correctly listed atoms