Hi Simon, The various output files are described in Chimera’s Autodock Vina documentation. As also mentioned in that page, when the docking results are returned they get opened up automatically: i.e. you do not have to explicitly open any files. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> That link is the copy on our website, but you should see basically the same page if you just click the Help button on the Autodock Vina dialog. If no results appeared automatically, the possibilities include: - job is still running - job failed for some reason, check Reply Log - job finished but zero results possible given the input structures/parameters I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: simon chapman <rowanlodge19@gmail.com> Subject: Re: [Chimera-users] substituting atoms Date: March 20, 2018 at 4:31:04 AM PDT To: Eric Pettersen <pett@cgl.ucsf.edu>
Many thanks Elaine and Eric, much obliged. Sorry if I got the protocol wrong!
5 files appear on my desktop after a docking run. One is the conf fie, the others are PDB or PDBQT files for ligand and receptor.
I'll keep battling, but perhaps cc.ing your colleagues will help. I'llet you know if the puzzle is resolved.
Simon
On 19 March 2018 at 17:26, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Simon, You should initially send these types of questions to the chimera-users list. I’m one member of a programming team and therefore not the expert on all aspects of Chimera — AutoDock Vina being one of the ones I’m not an expert on. I have cc’ed the team members who are the AutoDock Vina experts on this mail and one of them should be able to help out…
—Eric
On Mar 19, 2018, at 8:17 AM, simon chapman <rowanlodge19@gmail.com> wrote:
OK, me again....the Irish troublemaker.
I've been tinkering with the AutoDock Vina facility in Chimera Tools. All goes well until a pop-up asks me to specify a file type to open the resulting configuration file.
I have no idea what those abbreviations mean. I tried a few, but error messages appear every time.
Any thoughts? More beers if you can help.
Best wishes Simon
<vina 1.PNG> <vina 2.PNG>