BFEE VMD Plugin

[bhavranek]

I downloaded the BFEE VMD plugin and was looking to perform binding calculations for a protein-protein system. I noticed that it does not let me select the protein:protein option and only allows for the selection of the protein:ligand option. What is the reason for this?
What would be the best way to go about performing these calculations for a protein-protein system?

[HanatoK]

@bhavranek
I think it is simply that the protein-protein calculation is not implemented. Unlike the protein-ligand case, one needs to restrain the fluctuations of side chains of both proteins, and how to automatically determine the residues being restrained still puzzles us. Consequently, we have not implement the functionality yet. If you just want to apply a similar algorithm for a specific system, you could refer to dx.doi.org/10.1021/ct400273t.
@fhh2626 may have more hints about it.

[fhh2626]

@bhavranek protein-protein calculation is not implemented. However, you can start from the inputs generated for protein-ligand, and then modify the Colvars configurational files according to https://doi.org/10.1021/ct400273t.