Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.

Official Python client for accessing ChEMBL API.

Cloud-based molecular simulations for everyone

Calculate the binding free energy difference between two small molecules against the same protein target.

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.