Protein-protein interaction tutorial

User discussions
1

Hi,

I am learning how to use GROMACS and I am interested in protein-protein interactions.

I found the GROMACS tutorials very useful and I successfully went through them, however, I tried to adapt them for a protein dimer I am working on, and I found it somehow more challenging.

Can you suggest any tutorial that explains step by step how to run GROMACS with two proteins?

Is it also possible to use AlphaFold structures to do so?

Thanks for helping

Paolo

GROMACS version: GROMACS/2023.3-foss-2022a-CUDA-11.7.0
GROMACS modification: No

2

Can you first explain what you found challenging? Any errors you encountered? In principle having two proteins isn’t much different from having one, unless there’s something very peculiar about the desired setup.

Gromacs won’t care if your structure comes from a crystal, cryo-EM or AlphaFold, that’s a question of validity of the starting structure, and it’s hard to give a once-and-for-all answer without any details.

3

Create a two chain for the protein you wanted to simulate and pass through
gmx pdb2gmx
You will have the topoogy and system for the two proteins with different chain ID. Remaining procedures are same as other system