Energy minimization of hybrid ligand


I’ve got a hybrid ligand docked in the normal ligand binding site with no obvious steric clashes with surrounding residues.

I cannot get the energy to minimize on one of the ligand atoms. Is this an issue that others have experienced with hybrid molecules? Can it be due to the dummy atoms? Does anybody have a suggestion for steps to take?

Thank you,


Hey Dan,

it is difficult to say what exactly is happening there. It might be due to some distorted geometry that the docking program produces, as it likely has issues with understanding what a hybrid structure is. To avoid confusing the docking program, I would suggest to dock a non-hybrid ligand and generate hybrid structure afterwards.


Thanks Vytas,

I guess I shouldn’t say “docked”. I just set it up in a viewer according to a previously docked structure.

I have (seemingly) really high error values for my results. Are there things that typically cause high errors that I should be aware of or do I just need to up the number of transitions for each state?

Thanks again,