Hi, all I am refining a structure that has a metal-benzene coordination bond, usually the pdb was constructed in a way as seen in the crystal structure determined for the small molecule ligand. When I generated the .top and .param files, I usually could not define the bond between metal and the benzene since there is no specific atom this bond is supposed to be associated with. For most of the time it works ok in the refinement, the geometry remains reasonably constant, but in one of the structures I am refining, minimization keeps pushing the benzene away from the metal to a distance that is too far for coordination bond formation. I am guessing it is because there is not enough restraining descriptions in the .top and .param files to hold these two together. That is why I am wondering if there is anybody who knows how to deal with this kind of bond in cns refinement? But it could also be due to some other reasons that I am not aware of for now. Any information will be highly appreciated. Thanks!
Best, Peng
