#DelphiFroce Molecular Dynamics (DFMD)
DelphiFroce Molecular Dynamics is a tool to perform steered molecular dynamics simulations targeting receptor-ligand binding.
DelphiForce Molecular Dynamics utilize Amber Tools, NAMD and VMD to peform steered MD simulation and trajectory analysis, thus these packages should be installed before running the DFMD. The output trajectory generated from DFMD  will be in ./DCD/combine.dcd  

The script can be run from linux systems and require python version 3.4 or higher:
./python3 DelphiForce_MD.py + input parameters



Files needed in your working directory:
1. input pdb file for receptor
2. input pdb file for target
3. amber prepi and frcmod files for ligands. These files are topology files for MD simulation of ligand and can be generated by antechamber in Amber tools. These files should be put in SOURCE/parameters. The name should be ligandnamd.frcmod and ligandnamd_resp_gaff.prepi
DelphiForce_MD.py also need to read the MD parameters files in SOURCE folder. If the path to the SOURCE folder is changed, the new path should be specfied using the optional arguments -p  

DelphiForce_MD input parameters:
usage: DelphiForce_MD.py [-h] [-l SCALE_LOW] [-u SCALE_UP] [-n CYCLE_NUMBER]
                         [-f FORCE_UPDATING_FREQUENCY] [-c CUT_OFF]
                         [-d LANGEVIN_DAMPING] [-m {1,2,3}]
                         [-p PATH_TO_PARAMETERS_FILES] [-v PATH_TO_VMD]
                         [-a PATH_TO_AMBER] [-np NUMER_PROCESSOR]
                         receptor target


positional arguments:
  receptor              The receptor protein which the target will bind with.
  target                The target ligand which will bind with the receptor
                        protein.
optional arguments:
  -h, --help            show this help message and exit
  -l SCALE_LOW, --scale_low SCALE_LOW
                        The lower boundary in the force scaling. unit in
                        kcal/mol/Å. 1 kcal/mol/Å = 69.479 pN default = 0.2
                        kcal/mol/Å
  -u SCALE_UP, --scale_up SCALE_UP
                        The upper boundary in the force scaling. unit in
                        kcal/mol/Å. 1 kcal/mol/Å = 69.479 pN default = 1.18
                        kcal/mol/Å
  -n CYCLE_NUMBER, --cycle_number CYCLE_NUMBER
                        The number of Delphiforce calculation and updating
                        cycles in the simulation.default = 8000
  -f FORCE_UPDATING_FREQUENCY, --force_updating_frequency FORCE_UPDATING_FREQUENCY
                        The simulation running steps for each cycle. The
                        smaller running steps make the steered forces uppdated
                        more frequently. default = 500
  -c CUT_OFF, --cut_off CUT_OFF
                        The cut-off distance used in GBIS MD simulation.
                        default = 18 Å
  -d LANGEVIN_DAMPING, --langevin_Damping LANGEVIN_DAMPING
                        Langevin Damping coefficient used in GBIS MD
                        simulation. default = 1
  -m {1,2,3}, --simulation_mode {1,2,3}
                        Acceptable simulation mode: 1: Accelerated modeling.
                        The DelPhiForces are calculated and applied as steered
                        forces constantly until the end of simulation;
                        Accelerated modeling is the default simulation mode.
                        2: Cut-off modeling. the DelPhiFoces are
                        calculated and applied as steered forces only when
                        ligand atoms are far away from the receptor (exceed
                        the cut-off distance in MD simulation). 3: Scaled
                        modeling. When ligands atoms are within the cut-off
                        distance in MD simulation, the steered forces are
                        corrected as the substratcion of the Delphiforce and
                        MD forces to avoid double counting of the
                        electrostatic interactions in the simulation.
  -p PATH_TO_PARAMETERS_FILES, --path_to_parameters_files PATH_TO_PARAMETERS_FILES
                        path to the NAMD and Delphiforce executable files and
                        MD paramteres files.These files are orginally in
                        SOURCE folder. If the path to SOURCE folder is
                        changed, new path should be provided.
  -v PATH_TO_VMD, --path_to_vmd PATH_TO_VMD
                        path to the VMD executables files. DelphiForce MD
                        require Visual molecular dynamics(VMD) for trajecory
                        analysis. The path to VMD executables should be
                        provided.
  -a PATH_TO_AMBER, --path_to_amber PATH_TO_AMBER
                        path to the Amber Tools executables files. DelphiForce
                        MD require ambpdb and tleap from Amber tools to
                        generate amber parameters file and pqr file. The path
                        to Amber Tools executables should be provided.
  -np NUMER_PROCESSOR, --numer_processor NUMER_PROCESSOR
                        Number of processor core to run NAMD for the steer MD
                        simulation, which depends on the number of processor
                        core in your local machine.

EXAMPLES can be found in folder examples.       
