[Chimera-users] AutoDock Vina

[Elaine Meng]

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 at 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 at cgl.ucsf.edu] 
> Sent: Thursday, May 02, 2019 2:20 PM
> To: Hernando J Sosa
> Cc: chimera-users at 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 at 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&amp
>> ;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 at 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 at cgl.ucsf.edu> on behalf of 
>>> Hernando J Sosa <hernando.sosa at 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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