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PostPosted: Tue Feb 04, 2014 10:20 pm 
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Joined: Tue Feb 04, 2014 9:37 pm
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Hello,
I am a new user of AD4 and I want to do some post - processing of the docking results that requires all hydrogen to be present. I tried to add them back, but noticed that the bonding patterns are lost and using pymol for instance, results in the addition of 2 hydrogens to C's that should have only 1 (for instance in an aromat).

Is there any automated method to check the original input structures and add the hydrogens back to the .dgl or .pdb?

Thanks,
- Laura


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PostPosted: Mon Jan 19, 2015 9:32 pm 
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I am not sure whether I understand what you wrote. I usually save the ligand with desired conformation to PDB file. Then import it to PMV and add hydrogen atoms. And then save the PDB file.


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