Charmm scripts for QM/MM calculations


Scripts provided by Prof. Alex MacKerell Jr. Further explanations are given in the inputs.

  1. Setup QM/MM regions in NAD+ using frontier orbital approach, minimize and perform no4'-nc1'-nn1-nc2 torsional energy surface.

    nad_qm_surf_1a.inp
    ---top_all27_prot_na_qm.rtf
    ---par_all27_prot_na_qm.prm
    ---nad_qm_min.crd
    ---nad_qm_min_n180.crd

  2. Full molecule mechanics no4'-nc1'-nn1-nc2 torsional energy surface.

    nad_mm_surf_1a.inp
    ---nad_mm_min.crd
    ---nad_mm_min_n180.crd

  3. Set up propionaldehyde/NAD interacting pair, perform QM/MM setup, setup constraints and perform MD simulation. This is an example of how to due a QM based potential of mean force (PMF) calculation on a 2-dimensional reaction coordinate.

    nad_pral_qm_dyn_surf_2d.inp
    ---nad_pral_qm_min.crd