Bug in intramolecular and or unbound energy (original) (raw)

Using the vina or vinardo scoring functions, the unbound and intramolecular energy of the top pose should be equal. However, ligands with macrocycle closure atoms, which are CG0, G0, CG1, etc, show large discrepancies in these energies, sometimes leading to predicted free energies that are absurdely low, e.g. -50 kcal/mol.

REMARK VINA RESULT:   -17.786      0.000      0.000
REMARK INTER + INTRA:         -10.788
REMARK INTER:                 -10.720
REMARK INTRA:                  -0.068
REMARK UNBOUND:                17.397