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

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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.

4

Hi,

Thanks for the suggestion. I did try using the .pdb file instead, but it is not being shown as 2 separate chains. The protein I am working with has 175 residues each.

gmx_mpi make_ndx -f wt_dimer.pdb -o pocket.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 350 Protein residues
Analysing Protein…

0 System : 2918 atoms
1 Protein : 2918 atoms
2 Protein-H : 2918 atoms
3 C-alpha : 350 atoms
4 Backbone : 1050 atoms
5 MainChain : 1400 atoms
6 MainChain+Cb : 1728 atoms
7 MainChain+H : 1400 atoms
8 SideChain : 1518 atoms
9 SideChain-H : 1518 atoms

5

HI @athiras

If the two protein chains are separate entities then gmx make_ndx should be able to pick them up by typing splitch 1 which will split the chains contained in group 1 (the protein group).

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6

Hi @athiras,

Does the .pdb file contain the chain information? If the chain information is present, you should be able to select by, e.g., chain A.

Best,

Marius

7

Hi,
It worked. Thanks a lot!

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