WARNING: WARNING: Residue 27 named ALA Inquiry

User discussions
1

GROMACS version: 2020.3
GROMACS modification: Yes/No
Here post your question:
Hello I generating a molecular topology for the Umbrella Sampling Tutorial 3 and although successfully output the necessary complex.gro retrieved the below warning:

WARNING: WARNING: Residue 27 named ALA of a molecule in the input file was mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

Can anyone more specifically explain this warning?

Thanks:)

2

pdb2gmx sometimes prints out unnecessary information. If this is the last residue in the chain, then it’s just a sign that O is being replaced by an atom with a different name (like OT1, etc). If the topology is generated successfully, there’s nothing to worry about or troubleshoot.

3

Hello and ok thank you for the kind update:)