rdparm HTML documentation

The program is user driven, with various commands being typed in response to the rdparm prompt. To run the program, it is necessary to specify an AMBER prmtop file. If an AMBER prmtop is not specified on the command line (or incorrectly specified on the command line) the user will be prompted for a valid prmtop filename.

rdparm commands (in alphabetical order)

• ?:

  Type help information

• angles mask:

  List all the angles (involving any of the atoms in the mask, default: all atoms).

• atoms mask:

  List atom information, such as name, charge, residue name, etc. (involving any of the atoms in the mask, default: all atoms).

• bonds mask:

  List all the bonds (involving any of the atoms in the mask, default: all atoms).

• checkcoordinates filename:

  Read in the coordinate file specified in the filename, check for inconsistencies and print out a summary of the information.

• checkgrid filename:

  Read in the XPLOR formatted contour file (such as that generated with the ptraj grid command) and print out a summary of the density.

• checkmask mask:

  Process the atom mask listed in mask; this is used for debugging.

• delete [bond | angle | dihedral] number:

  Delete the bond, angle or dihedral numbered number from the prmtop. Although the prmtop is modified internally, the original prmtop is unchanged, hence to effect the changes write a new prmtop with the writeparm command. To figure out the numbering, use the bond, angle or dihedral command (with no arguments).

• deleteperturbed [bond | angle | dihedral] number:

  Same as above, but delete perturbed bonds, angles or dihedrals.

• dihedrals mask:

  List all the dihedrals (involving any of the atoms in the mask, default: all atoms).

• dumpdihedrals

  Dump out a summary of all the dihedral parameter types in the prmtop.

• exit

  Quit the program.

• help

  Print out help information.

• info

  Print out a summary of the information in the prmtop file.

• mardi2sander

  Convert mardigras restraints into sander style restraints. The user is prompted for necessary information.

• modifyboxinfo

  Modify the periodic box information. You will be prompted for information.

• modifymoleculeinfo

  Change the molecule information.

• newtransform script:

  Run the ptraj functionality.

• openparm

  Read in a different prmtop file.

• parminfo

  Like info, print out a summary of the information in the prmtop file.

• pertbonds mask:

  Like bonds, but applied to the perturbed bonds only.

• pertangles mask:

  Like angles, but applied to the perturbed bonds only.

• pertdihedrals mask:

  Like dihedrals, but applied to the perturbed bonds only.

• printbonds mask:

  Same as bonds.

• printangles mask:

  Same as angles.

• printdihedrals mask:

  Same as dihedrals.

• printatoms mask:

  Same as atoms.

• printexcluded

  Print out the excluded atom list.

• printlennardjones

  Print out a summary of the Lennard-Jones parameters.

• printtypes

  Print out the currently specified AMBER atom types.

• ptraj script

  Run ptraj

• quit

  Exit the program.

• readparm | rdparm

  Load up another prmtop file.

• restrain [bond | angle | dihedral ]

  Add in PARM type restraints; you will be prompted for atom numbers. This is not recommended as similar functionality is now within sander.

• scalebox

  This will scale all the coordinates in a given periodic box.

• stripwater

  This will strip water from a trajectory; it is recommended that ptraj be used to do this instead!

• system command:

  Use the system() call to run command (outside of rdparm).

• testwater

  Create a new prmtop that has a different number of water molecules.

• translatebox

  Shift coordinates (use ptraj instead!).

• translaterestrt

  Shift coordinates (use ptraj instead!).

• writeparm

  Output a new prmtop file.