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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Fri Feb 03, 2017 12:09 pm 
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Joined: Fri Nov 13, 2015 9:44 am
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Hi everyone,

for my docking procedure with Vina I have prepared the ligands with the proper protonation stats.
The pdbqt file, input as well as output files, only contain a few hydrogens. I suppose only the hydrogens of titratable groups which are protonated.

How can I convert such a pdbqt file into a pdb file which contain all hydrogens explicitly?

I have tried obabel with the -h option, but it adds all hydrogens whether it was (implicitly) present in the pdbqt file or not.
Also I dont want to use the -p option of obabel because it creates protonation states different than the ones which I used in the docking procedures. I want simply that the hydrogens which were implictly present in the pdbqt file become explicitly present. And if possible with a free commandline tool.

I look forward to hearing from you.

Best wishes,
Jadzia


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