I'm new to this list, but I saw in the archives that there was a thread on the shutdown of the Opal2 server. I wondered if there were any plans to make Autodock Vina available on alternate servers? Or if anyone knows of another way to access an Autodock Vina server? I have been using this server in a class for the past 5 or 6 years, so I'm keen to find an alternative option. kind regards, Kate
Hi Kate, Sorry, there are no plans on our part. Autodock Vina (and many other docking programs, DOCK etc.) are available for download and installation for running directly. <http://vina.scripps.edu/> <http://dock.compbio.ucsf.edu/index.html> Or if you wish to avoid installing any docking program yourself, there are at least a few docking web servers you could also run directly (independent of Chimera). I can't make a recommendation, but to mention a few: Dock Blaster, SwissDock, MTiAutoDock ... <http://blaster.docking.org/> <http://www.swissdock.ch/> <https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDo...> I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2020, at 11:48 PM, Kate Wegener <kate.wegener@adelaide.edu.au> wrote:
I'm new to this list, but I saw in the archives that there was a thread on the shutdown of the Opal2 server. I wondered if there were any plans to make Autodock Vina available on alternate servers? Or if anyone knows of another way to access an Autodock Vina server? I have been using this server in a class for the past 5 or 6 years, so I'm keen to find an alternative option. kind regards, Kate
Thanks Elaine. I have also found a web-server that runs Autodock Vina called Webina that I'm trialling. It creates an output file with extension *.pdbqt, but I can't work out how to open that in Chimera. Should it be possible? It asks me to select what type of file it is from an extensive list, but I don't see anything there that corresponds to Vina output. Any ideas? kind regards, Kate <http://researchers.adelaide.edu.au/profile/kate.wegener> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, 28 April 2020 12:21 AM To: Kate Wegener <kate.wegener@adelaide.edu.au> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Autodock Vina Hi Kate, Sorry, there are no plans on our part. Autodock Vina (and many other docking programs, DOCK etc.) are available for download and installation for running directly. <http://vina.scripps.edu/> <http://dock.compbio.ucsf.edu/index.html> Or if you wish to avoid installing any docking program yourself, there are at least a few docking web servers you could also run directly (independent of Chimera). I can't make a recommendation, but to mention a few: Dock Blaster, SwissDock, MTiAutoDock ... <http://blaster.docking.org/> <http://www.swissdock.ch/> <https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDo...> I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2020, at 11:48 PM, Kate Wegener <kate.wegener@adelaide.edu.au> wrote:
I'm new to this list, but I saw in the archives that there was a thread on the shutdown of the Opal2 server. I wondered if there were any plans to make Autodock Vina available on alternate servers? Or if anyone knows of another way to access an Autodock Vina server? I have been using this server in a class for the past 5 or 6 years, so I'm keen to find an alternative option. kind regards, Kate
Dear Kate The pdbqt (pdb+charges+torsions) file that VINA (an webina) produces are the poses of the ligand within the search area defined in the receptor. You could try to open this file extension in UCSF Chimera with the Tools > Surface/Binding Alaysis > ViewDock menu, it enables to open the pdbqt file extension. You need to load the receptor as well in order to give a glance of the docking results Regards El mar., 28 abr. 2020 a las 2:05, Kate Wegener (< kate.wegener@adelaide.edu.au>) escribió:
Thanks Elaine. I have also found a web-server that runs Autodock Vina called Webina that I'm trialling. It creates an output file with extension *.pdbqt, but I can't work out how to open that in Chimera. Should it be possible? It asks me to select what type of file it is from an extensive list, but I don't see anything there that corresponds to Vina output. Any ideas?
kind regards, Kate
<http://researchers.adelaide.edu.au/profile/kate.wegener>
------------------------------ *From:* Elaine Meng <meng@cgl.ucsf.edu> *Sent:* Tuesday, 28 April 2020 12:21 AM *To:* Kate Wegener <kate.wegener@adelaide.edu.au> *Cc:* chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> *Subject:* Re: [Chimera-users] Autodock Vina
Hi Kate, Sorry, there are no plans on our part.
Autodock Vina (and many other docking programs, DOCK etc.) are available for download and installation for running directly. <http://vina.scripps.edu/> <http://dock.compbio.ucsf.edu/index.html>
Or if you wish to avoid installing any docking program yourself, there are at least a few docking web servers you could also run directly (independent of Chimera). I can't make a recommendation, but to mention a few: Dock Blaster, SwissDock, MTiAutoDock ... <http://blaster.docking.org/> <http://www.swissdock.ch/> < https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDo...
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2020, at 11:48 PM, Kate Wegener <kate.wegener@adelaide.edu.au> wrote:
I'm new to this list, but I saw in the archives that there was a thread on the shutdown of the Opal2 server. I wondered if there were any plans to make Autodock Vina available on alternate servers? Or if anyone knows of another way to access an Autodock Vina server? I have been using this server in a class for the past 5 or 6 years, so I'm keen to find an alternative option. kind regards, Kate
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participants (3)
-
Elaine Meng -
JULIO MAZA VILLEGAS -
Kate Wegener