added tweak to write out the command line used for the conversion to the...

#    20161001   Added 'CMAP crossterms' section at the end of the data file

#    20161001   Added instructions in CMAP section to fix problem if 'ter'

#                 is not designated in the .pdb file to identify last amino acid

#    20161005   Added tweak to embed command line in generated LAMMPS input

#

#    General    Many thanks to Paul S. Crozier for checking script validity

#               against his projects.

    my $notes;

    $program            = "charmm2lammps";

    $version		= "1.9.0";

    $version            = "1.9.1";

    $year               = "2016";

    $add                = 1;

    $water_dens         = 0;

    $notes .= "      - project.in            suggested LAMMPS input script\n";

    $notes .= "      - project_ctrl.pdb      control file when requested\n";

    # record full command line for later use

    $cmdline = "$program.pl " . join(" ",@ARGV);

    foreach (@ARGV)

    {

      if (substr($_, 0, 1) eq "-")

  sub WriteLAMMPSInput

  {

    open(LAMMPS, ">$project.in");                       # input file

    printf(LAMMPS "# Created by $program v$version on %s\n", `date`);

    printf(LAMMPS "# Created by $program v$version on %s", `date`);

    printf(LAMMPS "# Command: %s\n\n", $cmdline);

    printf(LAMMPS "units           real\n");            # general

    printf(LAMMPS "neigh_modify    delay 2 every 1\n\n");

    printf(LAMMPS "atom_style      full\n");            # styles

      printf(LAMMPS "\n");

    }

    printf(LAMMPS "special_bonds   charmm\n");          # invoke charmm

    printf(LAMMPS "thermo          1\n");		# set thermo style

    printf(LAMMPS "thermo          10\n");              # set thermo style

    printf(LAMMPS "thermo_style    multi\n");

    printf(LAMMPS "timestep        0.5\n\n");		# 0.5 ps time step

    printf(LAMMPS "minimize 0.0 0.0 1000 10000\n\n");   # take off the edge

    printf(LAMMPS "timestep        1.0\n\n");           # 1.0 ps time step

    printf(LAMMPS "minimize 0.0 0.0 50 200\n\n");       # take of the edge

    printf(LAMMPS "reset_timestep  0\n");

    printf(LAMMPS "fix             1 all nve\n");

    printf(LAMMPS "fix             2 all shake 1e-6 500 0 m 1.0\n")

      if ($shake eq "");                                # shake all H-bonds

    printf(LAMMPS "fix             2 all shake 1e-6 500 0 m 1.0 a %s\n",$shake)

      if ($shake ne "");                                # add water if present

    printf(LAMMPS "velocity        all create 0.0 12345678 dist uniform\n\n");

    printf(LAMMPS "restart         10 $project.restart1 $project.restart2\n");

    printf(LAMMPS "dump            1 all atom 10 $project.dump\n");

    printf(LAMMPS "restart         500 $project.restart1 $project.restart2\n");

    printf(LAMMPS "dump            1 all atom 100 $project.dump\n");

    printf(LAMMPS "dump_modify     1 image yes scale yes\n\n");

    printf(LAMMPS "run             20\n");		# run for 20 time steps

    printf(LAMMPS "thermo          100\n");		# set thermo style

    printf(LAMMPS "run             1000\n");		# run for 1000 time steps

    close(LAMMPS);

  }