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PostPosted: Tue Jul 23, 2013 11:23 am 
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I would use vina to see how detergents interact with the hydrophobic domain of membrane proteins. In that case, how to make possible that more than 20 states could be estimated ? Could this number become a parameter to set up in the command line when running vina?
Thank you for your suggestions
Pierre


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PostPosted: Sat Jul 27, 2013 4:16 am 
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I am reposting this from the Vina mailing list:

From: Oleg Trott <trott@scripps.edu>
To: autodock@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.


I have recompiled vina in Linux (CentOS, Ubuntu and Fedora) and it works. I haven't been able to do it in Mac OS X.

Good luck!


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