Which protein-protein docking program? (Nonbonded interactions are usually included in the scoring function.)

If the proteins are treated as rigid bodies, the obtained complexes should be refined by molecular dynamics simulation, from which average electrostatic and van der Waals interactions between the two proteins can be obtained.

I used Cluspro for docking, and yes the obtained structures were treated as rigid bodies, and I am a bit new to Molecular Dynamics so I am planning to use GROMACS to refine the obtained complexes, electrostatic energy, and Vdw energy. so would be a right choice

From the docking results you get, usually you get a score or RMSD or ACE, these values ​​are used as interaction predictions. Visualization of docking results with DSV can also reveal residual interactions, types of interactions and bond distances.

DEAR Omar Soliman

Please consider these references such as

Energetic Aspects of Protein–Protein Interactions (PPIs)

• May 2021,DOI:10.1007/978-981-16-1594-8_3, In book: Protein-Protein Interactions

Computational Assessment of Protein–Protein Binding Affinity by Reverse Engineering the Energetics in Protein Complexes

• April 2021,Genomics Proteomics & Bioinformatics,DOI:10.1016/j.gpb.2021.03.004
• gOOD LUCK