Hello, In this context I want to that why the result of docking gives mangled ligand? I used web service mentioned in the last paragraph of Elaine's reply to Tunc. The poses listed in viewdock when observed in chimera main display, I found the ligand was not in its original structure. improper Bonds in ligand were added and its structure was mangled! What is the reason for this? -Robin Parmar PhD Research Scholar Dept of Zoology, Gujarat University India. On 1 April 2015 at 23:26, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hello Tunc, We do not have any control over your local installation, or whether you even have it installed locally! It is not included with Chimera. If you didn’t install it yourself, you should check with whoever did install it.

However, I could use the AutoDock Vina web service at NBCR successfully - I ran it just now in Chimera version 1.10.1 with the default server setting for the “Opal web service” option under Executable location. 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 Apr 1, 2015, at 9:02 AM, Tunc Morova <morovatunc@gmail.com> wrote:

...

Hello,

I was trying to use built-in auto dock vina tool of chimera. I came a cross with an error saying

service local`c:\”program filex(x86)”\”the scripps research Institute\Vina\Vina.exe` is unavailable.

I have been checking forums for a longtime. Unfortunately, i couldn’t run the docking. couple days ago, I think i accidentally ran the docking locally but i am not sure.

Is my pathing correct? how can my local auto dock vina be unavaible ?

Please help me for finishing my thesis :D

Thank you for your support

-Tunc

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users