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 Post subject: improving frequency
PostPosted: Mon Oct 26, 2015 3:53 pm 

Joined: Mon Jul 28, 2014 6:39 pm
Posts: 10
I would like to improve the frequency of the results of dockings. What I was trying to do is run the docking with a large box first, then download the file from the highest frequency from this and re-run the docking after de-selecting the ligand.

I am having trouble getting the box oriented for the second run. I think the box should appear where the ligand was, is this correct? Do you have any suggestions on how to do this efficiently?

Thanks


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 Post subject: Re: improving frequency
PostPosted: Mon Oct 26, 2015 7:36 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 203
Check the docked ligand coordinates in the downloaded file and use the average X, Y, Z for protein center - this is the most effective way to do this. However, if you ligand has high number of free torsions, it might be impossible to increase the frequency this way. In this case you might consider fixing some torsions of your ligand (modify tab on the ligand, allow rotation checkboxes)


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