Hi, I am trying to run QM/MM simulations on the RuBisCo enzyme. Babel converts xyz to txyz for the $molecule section, but with MM2 parameters. Is there a program available that automatically switches out MM2 with either CHARMM or AMBER parameters?
I do not know of one (doesn’t mean it doesn’t exist). I might recommend checking out the “CHARMMing” web portal (and several tutorials in journals). The portal and the tutorials were written in part by Lee Woodcock, who is the primary developer of the Q-Chem/CHARMM interface.
Have you tried Amber Tools?
I have created a custom Python script which uses the MDAnalysis Python package to generate Q-Chem QM/MM input files. My script is able to incorporate CHARMM parameters through specification of the PSF file and the CHARMM parameter files. It’s a bit clunky but gets the job done.
See here: GitHub - dahlpete/qmmm-qchem-setup: Collection of scripts for the automated setup of QM/MM simulations using Q-Chem.