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PostPosted: Wed Apr 23, 2014 9:44 pm 
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I have been using Autodock Vina for several months now, but I recently came across a youtube tutorial that adds polar hydrogens to the ligand on the step right after saving the pdbqt file of the protein, through AutoDock-tools.

Here's a link to the tutorial video, and I am referring to the (2:30 - 3:10) mark.

https://www.youtube.com/watch?v=LlPSQBDNFr8

I have never added polar hydrogens in this manner to my ligands. Is this a necessary step? Or is it only necessary for his tutorial since the ligand he is using is one he obtained from the pdb.org pdb-file, which is in turn, obtained from experimental crystallographic data - and therefore does not contain hydrogens?

Since I draw most of my ligands using Avogadro, and the drawn molecules do contain hydrogens when I save them as pdb files, does that make the step I am referring to in the tutorial unnecessary?

Thank you all for any clarifications,

-Saul


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PostPosted: Thu Apr 24, 2014 4:33 pm 
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AutoDock4 uses the United Atom model. This means only polar hydrogens are included in the coordinates file. However for correct partial charges, first add all hydrogens to the ligand to make sure the valencies of the heavy atoms are satisfied. When the ligand is written to a pdbqt file, the charge on each non-polar hydrogen is added to the charge of the heavy atom to which it is bonded and the non-polar hydrogen atom itself is removed from the molecule.

Adding only polar hydrogens to a molecule is ok for AutoDock Vina which uses the hydrogens only for setting atom types but wrong for AutoDock4


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PostPosted: Thu Apr 24, 2014 10:51 pm 
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thank you for the response.

If i understand correctly, Autodock 4 requires a few more steps, and treats hydrogens in a different manner than Vina (non-polar hydrogens are blended into the heavier atoms they are bonded to - and so are NOT included in the pdbqt file as individual atoms with their own coordinates - but polar hydrogens are included as individual atoms with their own properties and coordinates).

I use Autodock Vina. I am not sure I explained my situation correctly though. When I draw my ligand through Avogadro, I include all of the hydrogens in the drawing, and then save the ligand as a pdb file. Is there a step in the drawing process where I have to distinguish manually, which atoms are polar and which are not? I always figured that the distinction was made by the software itself, depending on whether the hydrogen atom was bonded to an electro-negative atom (such as oxygen) or not (such as carbon).


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PostPosted: Fri Apr 25, 2014 6:53 pm 
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Is there a step in the drawing process where I have to distinguish manually, which atoms are polar and which are not?

No, this is not necessary:
In your case, the molecules you draw "... do contain hydrogens when I save them as pdb files".
When each of these molecules is converted to pdbqt format, its non-polar hydrogens are removed.
Any hydrogens in the new pdbqt file will all be polar.

Vina uses the presence or absence of these polar hydrogens to assign atom types to some atoms.


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PostPosted: Fri Apr 25, 2014 8:17 pm 
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Thank you! You have clarified the issue for me.
:D


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