Different protein confirmations using gmx cluster

User discussions
1

GROMACS version:2021
GROMACS modification: No
Hi,
I have run 100ns md on a protein and now I want to use the gmx cluster command to get different conformations of the protein. So which group should be the best choice for least square fit and RMSD calculation.

2

Hi,
Difficult to generalise it depends on which questions you want to address with gmx cluster and and on your system.
Kind regards
Alessandra

3

Hi,
Thanks for the reply.
The main purpose of doing clustering is to get different conformation of protein and use it for virtual screening of small molecules.
So can you suggest which group should define this purpose most appropriately.

4

Protein conformational change is often described via changes in secondary or tertiary structure. For that, I would cluster based on the backbone. Side chains will flop around a lot even if the structure doesn’t change so those motions will obscure real, useful motions of the backbone. So don’t include them in the analysis.

5

Thanks for the suggestion.
I have one more question, my protein has a metal ion and pbc treatment with cluster option only provides the output with metal ion inside the protein while all other options show metal ion outside the protein. The metal ion parameter have been defined properly.
So my doubt is that can we consider pbc cluster output in this case as correct or i need to do it some other way,

6

Recenter on the protein chain with gmx trjconv and the metal should be wrapped together with it. Clustering is mostly useful for higher-order aggregates and assemblies.

7

Thanks for the suggestion.

But it didn’t work and metal atom is still show outside protein.

8

If the metal ion truly stayed coordinated, re-wrapping on the protein (assuming it is a monomer, if you’ve got a complex that’s a different story) should put everything into the unit cell correctly.

9

The issue is that pbc treatment using
mol and centering the protein option followed by gmx cluster gives me 7 clusters and the representative pdb of 2 clusters show metal ion outside the protein while 5 representative pdb show it at correct place.
So I tried all pbc removal options but only pbc cluster option worked giving 7 clusters with metal ion at its place.