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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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 Post subject: Vina in PyRx
PostPosted: Thu Feb 18, 2016 12:34 pm 
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Joined: Thu Feb 18, 2016 12:26 pm
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I started using the Vina in PyRx, at first I thought it did not generate output file in addition to the table with biding affinity values and RMSD as results. But yes! It generates an output file in C:\Users\PC\.mgltools\PyRx\Macromolecule as ligandname_out.pdbqt, instead of a dlg as in AutoDock.
The pdbqt file has coordinate bonding of the clusters and binding affinity values. This can be brought to ADT or PyMOL for visual details.
I got better affinity values using the Vina than AutoDock.

I hope for your helps


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