[Chimera-users] Non-alphanumeric character in keyword

MPI mpi566 at gmail.com
Tue Oct 27 10:42:57 PDT 2015


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 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.
> 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 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.
>>
>>
>> Thanks,
>> Dwey
>>
>>
>>> 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,
>>> Dwey
>
>



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