[Chimera-users] Non-alphanumeric character in keyword
mpi566 at gmail.com
Tue Oct 27 10:42:57 PDT 2015
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.
On 10/27/15, Elaine Meng <meng at 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.
> 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 at 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.
>>> On Oct 25, 2015, at 7:38 AM, MPI <mpi566 at 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,
More information about the Chimera-users