I want to calculate binding energy for a specially QM/MM minimised docked pose with partial charges for the ligand obtained from QM-level theory. When the pose is processed by the protocol, all ligand charges in the output molecule are set to zero. The protocol uses momany-rone rules for estimating charges for atoms of nonstandard residues in the CHARMm forcefield, so I added the ligand as new residue in the forcefield, but no luck. still zeros. What should I do ? 

Protocol Settings Protocol.pr_xml   Input Receptor Frame_5330.dsv Input Ligands Frame_5330.sd Input Group by Property   Flexible Receptor Atom Property Receptor.Positions,Gold.Protein.RotatedAtoms In Situ Ligand Minimization False Sphere of Flexible Atoms   Flexible Residues   Minimization   Minimization Algorithm Smart Minimizer Minimization Max Steps 1000 Minimization RMS Gradient 0.001 Minimization Energy Change 0.0 Ligand Conformational Entropy True Maximum Alignment RMSD 0.5 Conformation Generation   Conformation Method FAST Maximum Conformations 1000 Minimization   Minimization Minimization Algorithm Smart Minimizer Minimization Minimization Max Steps 500 Minimization Minimization RMS Gradient 0.1 Minimization Minimization Energy Change 0.0 Implicit Solvent Model Poisson Boltzmann with non-polar Surface Area (PBSA) Dielectric Constant 4 Implicit Solvent Dielectric Constant 80 Generalized Born Lambda Constant   Minimum Hydrogen Radius 0.8 Use Non-polar Surface Area True Non-polar Surface Constant 0.92 Non-polar Surface Coefficient 0.00542 Salt Concentration .145 Input Atomic Radii van der Waals radii Use Molecular Surface True Nonbond List Radius 14.0 Nonbond Higher Cutoff Distance 12.0 Nonbond Lower Cutoff Distance 10.0 Electrostatics Spherical Cutoff Kappa 0.34 Order 4 Advanced   Estimate Entropy True Entropy Temperature 298.15 Partial Charge Estimation Momany-Rone Parallel Processing True