Unable to select specific chains (A/B) for a dimer in v2024.3

User discussions
1

GROMACS version: 2024.3

Hi everyone,

I am trying to create an index group for the binding pocket of a dimer using GROMACS 2024.3. The pocket consists of a few specific residues.

When attempting to select the atoms, GROMACS does not recognize the “chain A” or “chain B” identifiers from my input structure.

Could someone advise on the correct syntax or the best alternative tools to properly index a binding pocket based on chain IDs?

Thank you.

2

Hi,

The problem could be that you are using a .tpr file for gmx make_ndx. Based on my knowledge, the .tpr format does not store chain ID information. I would recommend using a .pdb file as input for gmx make_ndx that contains the correct chain IDs.

All the best,

Marius

3

what was your inputs? please share the screen ouput too. you need to create a index of atoms with selected resides at the binding pocket.