How to calculate the binding energy from multimer complexes made by Alphafold2

[gundalav]

I have a structure created with Multimer option. The complex is created by giving the ligand and receptor amino acid sequences. I presume it is conceptually the same as 'docking'.

Is there a way I can calculate the binding energy for the complexes made by AF2?

G.V.

[HaoranHuang22]

You can check GROMACS

[gundalav]

Hi Hardlearn,

Thank you for your reply. I found GROMACS is heavy duty. I'm thinking simpler method, that I can command line, or programmatic like ProDy.

There's a web based tool called Prodigy. But since it's web based it's inconvenient, besides I'm not sure how accurate it is.

By the way, has anybody tested on Multimer output using GROMACS?

G.V.

[HaoranHuang22]

I have used GROMACS to calculate the binding energy for the output PDB format from alphafold2(colab version before alphafold-multimer existed), and now I am trying to use alphafold-multimer model to predict the structure of complexes and calculate the binding energy, and then compare them with previous results