How to separate multiple protein chains in the index file using Gromacs?

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No

How can I separate multiple protein chains (protein-protein complex structure) in the index file using make_ndx command?
Is it necessary to do this after creating the topology or after md simulation (just before analysis of rmsf)?
Thanks in advance

2

Hello,
If you have proper chain identifiers, you can use the “chain” option to choose your chain. eg. chain A
You can also choose the “r” option to select the residues or “a” to choose the atoms. eg. r 10-120