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Help to how to dock with flexible side chains?
http://mgl.scripps.edu/forum/viewtopic.php?f=12&t=3335
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Author:  Adellesigmund [ Wed Nov 02, 2016 11:11 am ]
Post subject:  Help to how to dock with flexible side chains?

I did rigid frame docking using vina for 2 protein subunits are closer, results are not that beneficial to me, so
desires to do flexible docking through choosing few residues close wherein I do expect some binding.
i have two pdbqt documents one with full model and some other with only residues that i'm interested. while jogging vina
I did get error message?
Prefix for bendy facet chains can be flex.pdbqt
Detected 2 CPUs
studying enter ...
Parse blunders online 1 in report flex.pdbqt: Unknown or irrelevant tag
Processing ligand 00131.nci_2 then it fails.

My query what are the approaches to do bendy docking? I do must hold handiest aspect chains no longer the primary chain?how to outline the residues in inflexible and flexible residues?
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