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PostPosted: Thu Dec 19, 2013 12:54 pm 
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I study docking by following Vina Video Tutorial <http://vina.scripps.edu/tutorial.html>, and these two how-tos:
http://autodock.scripps.edu/faqs-help/h ... -autodock4
and
http://autodock.scripps.edu/faqs-help/h ... -autodock4

I find, however, the receptor.pdbqt prepared by following vina tutorial and by following the two how-tos are different, and so is the ligand.pdbqt file. For the receptor.pdbqt, the only difference is the so called Gasteiger charge, where the deviation ranges from 0 (identical) to 0.02. For the ligand.pdbqt, the files resulted from two approaches share no similarity. Beside the different Gasteiger charges, the torsion trees (the root and branches), the order of atoms, and the number of active torsion are all different.

I wonder how to adjust the parameters to make identical results. Any suggestions are welcome.

Both approaches utilize MGLTools: Vina tutorial favors the GUI, but the how-tos prefer command line. I prefer command line because it is easy to be kept as record. Unfortunately, the result from command line produces ugly docking, in contrast to the GUI result, which produces docking commparable to the video tutorial. For all these results please check attached.


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PostPosted: Wed Feb 26, 2014 8:05 am 
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Well, I capture the true difference. In this case, the preparation made by command line (following the two how-tos) produces extra hydrogens, which are attached to three aromatic nitrogens. I think it is a bug, because (no matter these aromatic nitrogens are non-polar) aromatic nitrogens in a 6-membered aromatic ring should not connect to hydrogen.


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PostPosted: Wed Feb 26, 2014 6:37 pm 
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Using the -R flag to set the root atom set to zero seems to avoid adding hydrogens to the aromatic nitrogens (see the attached "new_ligand.pdbqt")

pythonsh prepare_ligand4.py -l ligand.pdb -R 0 -o new_ligand.pdbqt


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PostPosted: Thu Feb 27, 2014 2:20 am 
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Ruth Huey wrote:
Using the -R flag to set the root atom set to zero seems to avoid adding hydrogens to the aromatic nitrogens (see the attached "new_ligand.pdbqt")

pythonsh prepare_ligand4.py -l ligand.pdb -R 0 -o new_ligand.pdbqt



Yes, and even, the file "new_ligand.pdbqt" is almost the same as the one produced by GUI approach, except a slightly difference of a Q value for one atom. However, according the the meaning of root for atom tree, I don't think '-R 0' is a good choice in this case.


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PostPosted: Thu Feb 27, 2014 2:46 am 
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Ruth Huey wrote:
Using the -R flag to set the root atom set to zero seems to avoid adding hydrogens to the aromatic nitrogens (see the attached "new_ligand.pdbqt")

pythonsh prepare_ligand4.py -l ligand.pdb -R 0 -o new_ligand.pdbqt


I see. The critical option is '-A hydrogens_bonds'. In this case, polar hydrogen atoms is present in the original PDB, and need not added. If one insists on repairing the ligand, incorrect hydrogens are added, since MGLTools fails to detect some kinds of aromatic rings.

I repeat the same work with GUI of MGLTools, but this time I do add hydrogens, which is not done in the tutorial of Vina. And I notice the adding of unnecessary hydrogen atoms.

I guess only pure carbon aromatic rings can be correctly handled by MGLTools. Isn't it a bug?


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PostPosted: Thu Jan 08, 2015 4:31 pm 
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Using the -R flag to set the root atom set to zero seems to avoid adding hydrogens to the aromatic nitrogens (see the attached "new_ligand.pdbqt")

pythonsh prepare_ligand4.py -l ligand.pdb -R 0 -o new_ligand.pdbqt




___________
Arslan1


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PostPosted: Sat Jan 21, 2017 6:36 am 
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Using the -R flag to set the root atom set to zero seems to avoid adding hydrogens to the aromatic nitrogens (see the attached "new_ligand.pdbqt"). pythonsh prepare_ligand4.py -l ligand.pdb -R 0 -o new_ligand.pdbqt


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