Dear Elaine, Thanks for the suggestion but no main output. In GUI mode at Chimera ver 1.10.1, I can collect all 6 files but runing a script, I have 5 files and do NOT see mytest.pdbqt. Thanks, Dwey On 10/27/15, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Dwey, My guess is that you must be careful specify an output location where you have permission to write files, e.g. “output ~/Desktop/mytest”
Maybe when you used the GUI, you had browsed to such a location. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 27, 2015, at 8:51 AM, MPI <mpi566@gmail.com> wrote:
Dear Eric and Elaine,
Thanks for the solution.
It works but one of result files ( say, mytest.pdbqt if mytest is prefix) will NOT come out if the command of vina is provided in a script instead of GUI.
I guess that the main output ( mytest.pdbqt) will directly be given into viewdock in GUI mode and it will be saved but not in a script.
I wonder if there is a way to save the main output (mytest.pdbqt) in a script so that I can view the result of mytest.pdbqt later.
Thanks, Dwey
On Oct 25, 2015, at 7:38 AM, MPI <mpi566@gmail.com> wrote:
Dear users, In Chimera, I tried to run a vina docking in command line like
vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
There is an error:
Non-alphanumeric character in keyword 'search_center'
I have tried tweaking the keyword 'search_center' in different ways but the error won't go.
Dose anyone know how to fix it ? or is this format correct ? Many thanks, Dwey