Limitations of EDock?

[Carp_17]

Wondering if EDock currently has the capability to accept two ligands, one already inserted into a protein (thus, 1 ligand + 1 protein in the pdb file submitted to EDock) and the second as a lone Mol2 file. Is this possible to carry out, perhaps other than the method I've provided here?

[XiZhang]

Dear user, you may try merging one ligand and one protein into a single PDB file, making sure to change all record types to "ATOM". Then, submit both the merged PDB file and the MOL2 file to Edock. While this setup may allow the program to run successfully, please be aware that the energy function in Edock was not optimized for this particular scenario, and the results should be interpreted with caution.

Best,
Xi