The problem is that the GUI does a little extra work that the command line does not when you use the "Browse" button to select the output file, there is a checked check button (in small text) "add .pdbqt suffix if none given", so the file name that you supply actually has the .pdbqt appended automatically even if you do not type it. The command line, on the other hand, uses the value of the "output" option without modification and does NOT add the .pdbqt suffix. (I think the rationale is that you should be able to name your file exactly. Even the "add suffix" check button allows you to turn off that behavior. I'm not saying that's the RIGHT behavior, just that's the reasoning for the current behavior.) In any case, your command:
vina docking receptor #0 ligand #1 output mytest search_center 10,20,30
creates the output in file "mytest" rather than "mytest.pdbqt". I'm pretty sure if you say:
vina docking receptor #0 ligand #1 output mytest.pdbqt search_center 10,20,30
you should get the results in a properly named file. Conrad On 10/27/2015 8:51 AM, MPI 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 10/26/15, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
The file to be modified is <your Chimera installation>/share/Midas/midas_text.py. Here’s the diff:
@@ -3352,9 +3353,9 @@ except: raise MidasError, "No value provided for keyword '%s'" \ % typed - if not keyword.isalnum(): - raise MidasError, "Non-alphanumeric character in" \ - " keyword '%s'" % keyword + if not keyword.replace('_', '').isalnum(): + raise MidasError, "Non-alphanumeric or underscore " \ + " character in keyword '%s'" % keyword if keyword[0].isdigit(): raise MidasError, "Leading digit in keyword '%s'" % (
keyword)
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 26, 2015, at 6:43 PM, MPI <mpi566@gmail.com> wrote:
Dear Elaine,
Thanks for your kind help ! Would you please let me know which file is to be modified in old ver. if a single file is responsible for that keywords ? because I have mulitple manchines. I'll download a daily build and update that modifiled file if this would work.
Regards, Dwey
On 10/26/15, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Dwey, Sorry about that — it was a bug that keywords with underscores in them did not work.
You can get the fix in the next successful daily build (probably tomorrow). Check for daily build dated Oct 22, 2015 or later: <http://www.rbvi.ucsf.edu/chimera/download.html#daily>
Thanks for reporting the problem! 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 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
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