Dear Zhenyu, I don't know how to do this with pybel, but I remembered the program dimorphite_dl, and maybe that would be helpful to you.
The description states "Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range.": https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl Vin ________________________________ From: #MENG ZHENYU# via OpenBabel-discuss <openbabel-discuss@lists.sourceforge.net> Sent: Friday, December 2, 2022 12:44 AM To: openbabel-disc...@lists.sf.net <openbabel-disc...@lists.sf.net> Subject: [EXTERNAL] [Open Babel] add hydrogens appropriate for PH using Pybel Dear all, I’m trying to add hydrogens to the molecule with specified ph using Pybel, but it seems pybel cannot specify the ph. Do you have any idea how to do that? Your help will be highly appreciated! Best, Zhenyu **Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.
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