ADL: How can I get more that 20 binding modes

Luis De Leon huichoncito at yahoo.com
Fri Jul 12 22:27:43 PDT 2013


Thanks a lot Oleg
 
 Dr. Luis Manuel De Leon Rodriguez
Profesor Titular
Departamento de Quimica 
Universidad de Guanajuato


________________________________
 From: Oleg Trott <trott at scripps.edu>
To: autodock at scripps.edu 
Sent: Saturday, July 13, 2013 12:38 AM
Subject: Re: ADL: How can I get more that 20 binding modes
 

If you can re-compile Vina, you can change this line

par.mc.num_saved_mins = 20;

in main/main.cpp. Note that changing that "20" in the code changes the
algorithm somewhat, and not just the output.

Alternatively, without re-compiling, if you normally run Vina with
exhaustiveness=8, you can instead run it 8 times with exhaustiveness=1
and collect up to 20 conformations from each run, which may or may not
be the same between runs.

On Thu, Jul 11, 2013 at 3:10 PM, Yahoo <huichoncito at yahoo.com> wrote:
> Yes this is about autodock vinaa
>
> Luis M. De Leon Rodriguez
>
> On Jul 12, 2013, at 5:52 AM, Oleg Trott <trott at scripps.edu> wrote:
>
>> Is this about AutoDock Vina?
>>
>> On Thu, Jul 11, 2013 at 8:38 AM, Luis De Leon <huichoncito at yahoo.com> wrote:
>>>
>>>
>>> I am running some dockings using very small molecules, and I would like to get as many binding modes as possible. It seems that autodock is limited to a maximum of 20 binding modes is there anyway to get more than 20 binding modes?
>>>
>>> Thanks
>>> Dr. Luis Manuel De Leon Rodriguez
>>> Profesor Titular
>>> Departamento de Quimica
>>> Universidad de Guanajuato
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>>
>>
>> --
>> Oleg Trott, Ph.D. (Columbia University)
>>
>> Staff Scientist in the Olson Lab
>> The Scripps Research Institute
>>
>> http://olegtrott.com
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com
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