[Chimera-users] Loop through pbd files (ligand poses) and find hydrogen bonds against one template receptor

Samuel Kyobe samuelkyobe at gmail.com
Wed Apr 13 05:36:13 PDT 2022

Dear Chimera (and ChimeraX) team

I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation.

I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. 

In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file.



Dr. Samuel Kyobe 
Department of Medical Microbiology,
3rd floor, Pathology/Microbiology BLDG,
School of Biomedical Sciences
College of Health Sciences,
Makerere University.
Box 7072, Kampala, Uganda.
Mob: +256775468605 
Skype: samuelkyobe

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