Hi Hernano, As I mentioned before, you cannot change the limits in the GUI. You would have to use the “vina” command. Best, Elaine
On May 2, 2019, at 1:49 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine. I downloaded&installed Vina in my computer and I can use it from chimera (Tools -> Autodock Vina -> Advanced Options -> Executable Location -> Local) but still don't know where to change the maximum number of models. The GUI (Tools -> Autodock Vina -> Advanced Options -> Number of Binding Modes) doesn't go higher than 10 after even after setting it to use the local version. ??
Best
Hernando
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Thursday, May 02, 2019 2:20 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] AutoDock Vina
Update: I’m told that the limits in the Chimera “Autodock Vina” GUI are the limits from the web service that is used, but if you use the command implementation “vina” in Chimera with a local installation of Autodock Vina, you should be able to use larger numbers. I will correct the documentation so that it doesn’t say num_modes maximum for the command is 20.
Elaine
On May 2, 2019, at 10:41 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Hernando, The Chimera tool named “Autodock Vina” just connects to an outside web service (at a different lab, not at UCSF) that is running Autodock Vina. Because it is a shared resource, this web service does not allow very much sampling of space, and it only allows docking one small molecule at a time.
The dialog choices only go up to 10. I believe if you use the “vina” command implementation (uses same web service) you can specify num_modes up to 20, but that is still relatively low compared to what is used in general practice.
<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvina%2Fvina.htm l&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C66e36a5c1c6845e 107fa08d6cf2ad337%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C6369241 80171787042&sdata=G3wCcOPiDcoz%2Bx68NYYl5H0YbjT8O%2B9QTRpY1jeylug% 3D&reserved=0> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww. rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fvina.html&da ta=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C66e36a5c1c6845e107fa08d 6cf2ad337%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636924180171787 042&sdata=J29ntMdcB36%2BJOznWMs%2Ft%2FQ22FPWfbj6kIMYvcccrXI%3D& ;reserved=0>
To do better (more intensive) sampling of space, and/or dock a lot of small molecules in a database-search mode, we recommend downloading Autodock Vina and running it directly. It is more work to learn how to use it directly, but then you have full control by using the config file that Ibrahim mentions, as needed for most research projects.
Autodock Vina website: <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvina .scripps.edu&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C66e3 6a5c1c6845e107fa08d6cf2ad337%7C04c70eb48f2648079934e02e89266ad0%7C1%7C 0%7C636924180171787042&sdata=zN2L1upQNfSWzOX2U2xGEke9rG3bgQkpFFuw4 baOJsk%3D&reserved=0>
The Chimera dialog and command can also be told to use a local installation, but to the best of my knowledge they are still limited to the same num_modes as mentioned above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 2, 2019, at 7:40 AM, Moustafa, Ibrahim M. <ria2@psu.edu> wrote:
Yes. In the config file you can set the "num_modes" parameters to the number you want.
e.g. num_modes = 15
Ibrahim
From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Hernando J Sosa <hernando.sosa@einstein.yu.edu> Sent: Wednesday, May 1, 2019 10:20 PM To: Chimera Subject: [Chimera-users] AutoDock Vina
Is it possible to specify more than 10 'Number of Binding models' on the AtoDock Vina dialogue?
Thanks Hernando
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