How to use Tinker to generate inputs with force fields for Lammps simulations

  • generate a tinker format xyz file
    • ~/projects/bin-macos/pdbxyz file.pdb
  • change the numeric types in the xyz file (to those in PRM )
  • ~/projects/bin-macos/minimize P4_CH3.xyz, with the PRM file –> .xyz_2
  • use charges from ORCA to update the PRM file
  • redo minimize –> .xyz_3
  • ~/projects/bin-macos/analyze P4_CH3.xyz_2 Moreno.prm P > out
  • remove the useless header ### in out
  • python tinkertoLAMMPS.py
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