Make index file for each residue

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1

GROMACS version: 2023.3
GROMACS modification: No
Here post your question

I would like to make an index file with atoms in each residue as a separate group. Say, residue 1 has atoms 1-10, residue 2 has atoms 11-20 and so on.
I would like to define groups such that [ group 1 ] has 1-10 atoms, [group 2 ] has 11-20 atoms.
When I run gmx make_ndx and use the “splitres” option, each residue is created as a separate group but only the first atom of the residue appears in the group.

Can someone please help me in building the residue-wise groups.

Thanks,
Raman

2

you can create using the index or residue id.

3

I understand that but doing this for files with several hundreds of residues will be time consuming.

4

It is a bug in both 2023 and 2024 version. Fix should be out soon, here you can find the patches

1 Like
5

Thanks @obZehn. This was indeed helpful.