#The outputs for each example are *.out files or the out directory.


QMMM_select: select QMMM region from a .gro file.
    ./master-qmmm-select 310alpha19.gro


QMMM_inp: generate PQS input files and do DFT-D3 calculation.
   ./master-QMMM-inp_PQS_D3 310poly3.pxyz


gen_ref: generate ref file using forces from PQS and DFT-D3
   ./ala_get_ref 310poly3.pxyz 


off2ff_copy:copy fitted parameters from .off to .ff.
   off2ff proto.copy inter.off intra_template.ff intra.ff


off2ff_condition: condition based update
   off2ff proto.condition intra.off intra_template.ff intra.ff


off2top_1:updat nonbonded list, generate tabulate potentials and update parameters in [ atoms ], [ bond ], [angle] and [dihedral] sections
   follow the workflow in the directory, the outputs are in out directory, the top directory contains the .top as an example.


off2top_2:updat nonbonded list, generate tabulate potentials and update parameters in [bondtypes],[angletypes] and [dihedraltypes] and charges in [ atoms ] under [moleculetype].
   follow the workflow in the directory, the outputs are in out directory, the top directory contains the .top as an example.


QMMM_translation_file: template translation files for scripts generating QMMM calculations
off2ff_protocol: protocols for updating a .ff file from a .off file.
