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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Tue Oct 27, 2015 7:36 pm 
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Joined: Mon Oct 05, 2015 4:12 pm
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Hello
I have just started using Vina to perform virtual docking of small ligands on a receptor protein with a known binding site. I specify the gridbox dimensions in the configuration file. However, a large number of the models show the ligand binding outside the specified gridbox. This doesn't happen when I perform docking of individual ligands on the receptor using the autogrid/autodock routines of autodock. What further restrictions should I include in the Vina configuration file to limit the docking to the specified gridbox dimensions? Thank you


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