Dear Chimera, Dear Chimera, I am trying to use your software to run molecular docking of sucrose onto a structure. I've provided the ligand and also the receptor structure in the email. I've added the charge for the ligand (using Tools->Structure editing-> Add charge) and selected Gasteiger ad the charge method. After that, I prep the ligand (using Tools -> Structure editing-> Dock Prep). Then, I performed the docking thru Tools ->Surface/Binding Analysis ->AutoDock Vina. Vina program managed to run, but with some errors. The ligand bound to the structure is not the right structure of sucrose, but a hairball. I suspect there's something wrong with the Ligand prepping method in chimera that causes the structure to go crazy. Can you help me with this problem? Many thanks, Su