in the docking process this message appear and does not continue, opal:vina_1.1.2 unavailable what i should do
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
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
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
The last half of my previous message already suggested one possibility for using a different web server to run the calculation and then opening the results in the Chimera ViewDock tool, which allows checking for H-bonds etc. If that doesn't work, you will have to figure out something on your own. Elaine
On Apr 30, 2020, at 10:44 AM, Ahmed Tawfeek <ahmed_tawfeek83@yahoo.com> wrote:
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
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- M.C Gabriel Salazar Robles Estudiante de Doctorado en Biotecnología en la UPAEP Profesor de asignatura en la Universidad Politécnica Metropolitana de puebla Cel/WhatsApp: 2228 33 54 58 Email: gabrielsrbio@gmail.com
participants (3)
-
Ahmed Tawfeek -
Don Gabo -
Elaine Meng