Dear Elaine, Thank you very much Elaine, but i could get the interactions and bonds could you help me or guide me for another option

waiting your reply ahmed On Thursday, April 30, 2020, 05:11:15 PM GMT+2, Elaine Meng meng@cgl.ucsf.edu wrote:

Sorry, the Autodock Vina web service is no longer available.

This was already discussed on the mailing list

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016738.html http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016752.html

and is also shown on the Help page for this tool:

http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html

Somebody on the mailing list mentioned that there is another Autodock Vina web server called Webina https://durrantlab.pitt.edu/webina/

...that you may be able to use directly (not in Chimera).  I have not tried it myself, but according to others, after you get the output file from Webina you may be able to open and view it with the ViewDock tool in Chimera as described in the second message below:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016762.html http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016764.html

Elaine ----- Elaine C. Meng, Ph.D.                      UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Apr 30, 2020, at 6:37 AM, Ahmed Tawfeek ahmed_tawfeek83@yahoo.com wrote:

Dear Professors and Doctors, I need the help I am trying to learn the work on chimera for the purpose of checking my compounds as organic chemist but i could not continue, because at the docking stage, the autodock vina does not work and this message appear,

the message " opal:vina_1.1.2 unavailable"

what is the solution

Best Regards

Ahmed Tawfik

Thank you.

Was investigating and I solved the problem by the following way:

Download and install the AutoDock Vina app from this website: http://vina.scripps.edu/download.html , then go to Tools-> Surface/Binding Analysis->AutoDock Vina, click on it, then go to "Executable Location", click on "Local", then in "Browse" and look for the executable file "vina.exe" of the recently installed AutoDock Vina (I found it on C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe), click on it and then "Ok" in the AutoDock Vina window of Chimera.

I got to use the AutoDock Vina function as it was with the website, no changes in performance and no need for uploading receptor/ligands nor downloading docking files.

Best regards!

On Thu, Apr 30, 2020 at 10:11 AM Elaine Meng meng@cgl.ucsf.edu wrote:

Sorry, the Autodock Vina web service is no longer available.

This was already discussed on the mailing list

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016738.html http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016752.html

and is also shown on the Help page for this tool:

http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html

Somebody on the mailing list mentioned that there is another Autodock Vina web server called Webina https://durrantlab.pitt.edu/webina/

...that you may be able to use directly (not in Chimera). I have not tried it myself, but according to others, after you get the output file from Webina you may be able to open and view it with the ViewDock tool in Chimera as described in the second message below:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016762.html http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016764.html

Elaine

Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Apr 30, 2020, at 6:37 AM, Ahmed Tawfeek ahmed_tawfeek83@yahoo.com

wrote:

...

Dear Professors and Doctors, I need the help I am trying to learn the work on chimera for the purpose of checking my

compounds as organic chemist but i could not continue, because at the docking stage, the autodock vina does not work and this message appear,

...

the message " opal:vina_1.1.2 unavailable"

what is the solution

Best Regards

Ahmed Tawfik

---

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