ADL: HydrogenBondBuilder Error - Unable to assign HYB type to atom N

Jared Hass jhass2 at huskers.unl.edu
Wed May 20 07:51:58 PDT 2020


Hello,

My name is Jared Hass and I am a graduate student at the University of Nebraska-Lincoln. I am trying to use some of the python files from the MGLTools v 1.5.7 in the /MGLToolsPckgs/AutoDockTools/Utilities24 folder. I was specifically looking at the summerize_results.py file. I am supplying this python code a .dlg and the rigidReceptor.pdbqt file that was created from autogrid. I do not encounter any errors in the python file, but for some reason it is unable to produce any hydrogen bonds. The only thing that  is printed is Unable to assign HYB type to atom X.

I do have this file copied in another folder and am executing it there. I am sourcing the .../mglenv.sh prior to running the code and have no import errors. Is there a common issue with this or am I not providing the right rigidReceptor file? I have tried the origional protein.pdbqt and get the same issue. I have been using AutodockFR to do all the receptor preparation and creation of the map files and autodock seems to take these files no issue.

Is there way to troubleshoot this code by going into the Molkit/hydrogenBondBuilder.py file? Or is there a way to see why I am getting 0 hydrogen bonds for any ligand?

Thank you for your time and assistance,

Jared L. Hass


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