"rdparm

In the commands below, text in "<>"'s represents arguments to the command. Within the parenthesis (<>), quotes surround words that are typed verbatim and the "||" string represents an "or" or separates various possibilities for the verbatim text. The argument refers to a specification of the atoms based on the format used by midas. In this, residues and atoms can be referred to by number or name. The ":" is the residue specifier, "@" an atom specifier, "?" a single character wild card, "-" a continuation character, and "*" a multicharacter wildcard. The processor is crude at best!

?

Print the help file. If an argument is given, help is printed for this command.

angles

Print all the angles in the file. If the is present, only print angles involving these atoms. For example, atoms :CYT@C? will print all angles involving atoms which have 2-letter names beginning with "C" from "CYT" residues.

atoms

Print all the atoms in the file. If the is present, only print these atoms.

bonds

Print all the bonds in the file. If the is present, only print bonds involving these atoms.

checkcoords

Perform a rudimentary check of the coordinates from the filename specified. This is to look for obvious problems (such as overflow) and to count the number of frames.

dihedrals

Print all the dihedrals in the file. If the is present, only print dihedrals involving one of these atoms.

ddrive

Create an input file for the SPASMS dihedral driver.

delete

This command will delete a given bond, angle or dihedral angle based on the number specified from the current prmtop. The number specified should match that shown by the corresponding print command. Note that a new prmtop file is not actually saved. To do this, use the writeparm command. For example, "delete bond 5" will delete with 5th bond from the parameter/topology file.

delperturbed

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

restrain

This is a means to add restraints as is possible with the "parm" program. Its usage is somewhat obsolete because more flexible restraints can be specified with the NMR functionality of sander. To use this command, specify whether the restraint is to a bond, angle or dihedral and the program will prompt for atom numbers (as specified in the "atom" or "printatom" command). As before, the prmtop is not actually saved until a "writeparm" command is issued.

openparm

Open up the prmtop file specified.

writeparm

Write a new prmtop file to "filename" based on the current (and perhaps modified) parameter/topology file.

system

Execute the command "string" on the system.

mardi2sander

A rudimentary conversion of Mardigras style restraints to sander NMR restraint format.

rms

Create a 2D RMSd plot in postscript or PlotMTV format using the trajectory specified. The user will be prompted for information. This command is rather slow and should be integrated into the "ptraj" code, however it hasn't been yet.

stripwater

This command will remove or add three point waters to a prmtop file that already has water. The user will be prompted for information. This is useful to take an existing prmtop and create another with a different amount of water. Of course, corresponding coordinates will also have to be built and this is not done by "rdparm". To do this, ideally construct a PDB file and convert to AMBER coordinate format either with carnal or "ptraj".

ptraj

This command reads a file or from standard input a series of commands to perform processing of trajectory files. See the supplemental documention.

transform

Perform rudimentary trajectory processing; this command is obsolete.

translateBox

Translate the coordinates (only if they contain periodic box information) specified to place either at the origin (SPASMS format) or at half the box (AMBER format).

modifyBoxInfo

This is a command to modify the box information, such as to change the box size. The changes are not saved until a writeparm command is issued.

modifyMolInfo

This command checks the molecule info (present with periodic box coordinates are specified) and points out problems if they exist. In particular, this is useful to overcome the deficiency in edit which places all the "add" waters into a single molecule.

parmInfo

Print out information about the current prmtop file.

pertbonds, perturbedBonds

Print out the perturbed bonds.

pertangles, perturbedAngles

Print out the perturbed angles.

pertdihedrals, perturbedDihedrals

Print out the perturbed dihedrals.

printAngles

Same as "angles".

printAtoms

Same as "atoms".

printBonds

Same as "bonds".

printDihedrals

Same as "dihedrals".

printExluded

Print the excluded atom list.

printLennardJones

Print out the Lennard-Jones parameters.

printTypes

Print out the atom types.

quit

Quit the program.

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