On Mar 20, 2017, at 10:52 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
One thought is that maybe although the structure you are viewing is a trimer, what was returned by the receptor-prep script and actually used in the docking calculation was some smaller set of atoms, such as only the monomer. If you entered “/location/name” as the output file in the Chimera dialog, then this prepared receptor file would be /location/name.receptor.pdbqt. You should open this file in Chimera, and verify that it contains the receptor atoms you expected. (I do not know if this prep script handles multimers correctly.)
P.S. It may also depend on how you generated the trimer. In the Chimera dialog for AutoDock Vina, you have to specify a single model as the receptor. If you made the trimer from the monomer using the “sym” command, for example, it could be more than one model, so you would have to combine them first. This could be done with the “combine” command or with the “copy/combine” function in the Model Panel. However, this is not relevant if your trimer was already a single model. Elaine