Hi Mariana, Sorry for the difficulties. I can reproduce the problem with prep-script options not being recognized, as well as wrong-looking results (ligand intersecting receptor) from running the vina command. However, I find that results vary regardless of whether I’m running the command-line or GUI, perhaps more evident since I was using low exhaustiveness for testing. I thought that there was some randomization during the search so one wouldn’t necessarily expect identical results from identical input parameters. I.e. re-running with the same inputs and parameters from the GUI does give me different results each time. However, I didn’t see wrong-looking results from GUI runs, so as far as I know the problems are restricted to command-line execution. Anyway, we will have to look into these issues as time permits; thanks for reporting them, and sorry again for the inconvenience. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 13, 2018, at 6:25 AM, Mariana Assmann <mariana.assmann@gmx.net> wrote:
Hi everyone,
I am trying to do docking using the command line tool in chimera. I found that when I use the GUI opening Tools > Surface/Binding Analysis > AutoDock Vina and following the docking window, I get very similar results for the docking pose and score every time I run the docking. However, if I do the same with the command line tool (with the same parameters, box size, local version of vina, same dock prep), I get very different results: the ligand is never in a good docking position, always on a different side of the pocket, and sometimes even intercepts strands of the protein. The docking scores are also off.
I am using using Chimera 1.13 (build 41780), AutoDock Vina 1.1.2 (May 11, 2011), and the following command line for docking:
vina docking receptor protein ligand #1.2 output /home/mariana/GTN/docking/keap1/docking_test13 search_center -7,3,-30.32 search_size 19,21,21 backend local location /home/mariana/bin/vina num_modes 9
I also found that the command line does not accept any of the vina receptor or ligand options (e.g. receptor_addh) and gives me error messages when including those ("Keyword 'receptor_addh' doesn't match any known keywords")
Does anyone what the problems for those issues could be?
Thanks, Mariana