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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Wed Apr 10, 2013 4:39 pm 
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Millimolar User
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Joined: Wed Apr 10, 2013 4:35 pm
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Hi..
I have successfully completed vina dock run but i want to know that how i can view the ligand conformation along with pdb and its interaction so that i can find H-bonds between ligand atom and its corresponding amino acids.

Also please help me to run 10 ligands against a single pdb in vina.

Thanks...


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PostPosted: Tue May 07, 2013 7:40 pm 
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Micromolar User
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Joined: Tue Sep 21, 2010 10:56 am
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In case you are on Linux use pymol trugh command:
pymol out.pdbqt receptor.pdbqt
Other viewers are not happy about qt part, but you can try to trick them by rename .pdbqt->.pdb, or even better with Linux conversion command:
cut -c-66 my_docking.pdbqt > my_docking.pdb
On windows you have to use notepad to delete last 2 columins from pdbqt file then save it as pdb.


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