[Chimera-users] Tutorials

Bobby Barnett bobby.barnett at gmail.com
Sat Mar 28 11:25:07 PDT 2015

Dear Elaine,

Thanks for the advice about using the Autodock Vina option under
Surface/Binding Analysis.  I have run this with both the web based option
and the local option and get  the same error "[Errno 13] Permission denied:
'trial.receptor.pdb'"  I don't see a way around this error.  Do I need to
run the program as Administrator?

Thanks again for your help.

Bobby Barnett

On Fri, Mar 27, 2015 at 1:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Bobby,
> You’re welcome.
> We don’t have a tutorial for the Autodock Vina interface, but there is a
> manual page.  It should be reasonably friendly if you open the ligand and
> receptor as two separate models (from two separate input PDB files) and
> just fill in the required fields in Chimera’s Autodock Vina dialog,
> including drawing a box with the mouse in the main window to define a
> search area.
> See the manual page for explanations of the fields in the dialog:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> Looking at other (non-Chimera) tutorials might be confusing because they
> are not describing using this interface in Chimera.  They might be useful
> for explaining what the advanced parameters mean, but you wouldn’t want to
> try to follow them step by step.  Also keep in mind that Autodock is a
> different program from Autodock Vina.
> I hope this helps,
> 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 Mar 27, 2015, at 7:01 AM, Bobby Barnett <bobby.barnett at gmail.com>
> wrote:
> > Dear Elaine,
> >
> > I meant to thank you earlier for the many tutorials you provided, but I
> got distracted.
> >
> > I did have another question and i will post it on the regular way if it
> is needed, but is there a tutorial using the Autodock Vina under the tools
> Surface Binding Analysis option?  I have tried several times to perform
> this with one of the autodock tutorials and can't get it to work under
> chimera.
> >
> > Thanks again for your help.  I really appreciate all of the tutorials
> and the videos that you and your group provide.
> >
> > Bobby Barnett, semi-retired crystallographer
> >
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