How can I calculate the free energy of binding of a MOE database obtained from a molecular dynamics simulation of a protein-ligand complex? Thank you.
Ricardo J Ferreira
In MOE you can calculate Free Energies of Binding through the Thermodynamic Integration method (but requires AMBER):
https://video.chemcomp.com/watch/jMbR79BBtsjmp5wz64ETez
Another way is to export topologies and trajectories to PDB/DCD (or XTC, via VMD for instance) and use gmx_MMPBSA:
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.3/
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