Tool for automatically adding hydrogen atoms to dangling bonds

1

Hello,

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

Thank you!

2

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,

Tom