Tool for automatically adding hydrogen atoms to dangling bonds


I was wondering if there is any tool in ChemShell that can automatically add hydrogen atoms to dangling bonds?

Thank you!

Hi asoyemi,

There is no general tool as such but there is some functionality to do this in specific situations:

  1. The QM/MM module in both Tcl-ChemShell and Py-ChemShell will analyse the QM region defined by the user and automatically add hydrogen link atoms to the QM model where covalent bonds have been cut.

  2. Py-ChemShell contains a wrapper to the PDB2PQR utility which can add missing hydrogen atoms to experimental crystal structures of biomolecules in PDB format. See: The solvation workflow: setup — Py-ChemShell 21.0.1 documentation

Hope that helps,