ptraj/rdparm HTML documentation

NOTE: This documentation is out of date; please see the up-to-date documentation and versions of rdparm/ptraj in the AmberTools suite available at

The current version of ptraj (previously called rdparm) is really two programs:

Which code is used at runtime depends on the name of the executable (note that both rdparm and ptraj are created by default from the same source code when the supplied Makefile is used). If the executable name contains the string "rdparm", then the rdparm functionality is obtained. rdparm is semi-interactive (type ? or help for a list of commands) and requires specification of an AMBER prmtop file (this prmtop is specified as a filename typed on the command line; note that if no filename is specified you (the user) will be prompted for a filename). For more information about rdparm follow this link to rdparm.html.

If the executable name does not contain the string "rdparm", ptraj is run instead. ptraj also requires specification of parameter/topology information, however it currently supports both the AMBER prmtop format and CHARMM psf files. Note that the ptraj program can also be accessed from rdparm by typing ptraj (or newtransform). The commands to ptraj can either be piped in through standard input or supplied in a file, where the filename (script) is passed in as the second command line argument. Note that if the prmtop filename is absent, the user will be prompted for a filename.

ptraj: process trajectories...

ptraj is a program to process and analyze sets of 3-D coordinates read in from a series of input coordinate files (in various formats as discussed below). For each coordinate set read in, a sequence of events or actions is performed (in the order specified) on each of the configurations (set of coordinates) read in. Trajectory files can also be output.

To use the program it is necessary to (1) read in a parameter/topology file, (2) set up a list of input coordinate files, (3) optionally specify an output file, (4) specify a series of actions to be performed on each coordinate set read in, and <5> optionally analyze any accumulated results.

As mentioned above, input to ptraj is in the form of commands listed in a script (or if absent, from text on standard input). An example input file to ptraj follows:

trajin traj1.Z 1 20
trajin traj2.Z 1 100
trajin restrt.Z
trajout fixed.traj
rms first out rms @CA,C,N
center :1-20
strip :WAT

This reads in three files of coordinates (which can be compressed and the type is autodetected), a trajectory file is output (by default to AMBER trajectory format), rms fitting is performed to the first coordinate frame using atoms names CA, C and N (storing the RMSd values to a file named "rms"), the center of geometry of residues 1-20 is placed at the origin, the coordinates are imaged (which requires periodic boundary conditions) to move coordinates outside the periodic box back in, and then the coordinates of all the residues named "WAT" are deleted.

ptraj command prerequisites:

Before going into the details of each of the commands, some prerequisites are necessary to describe standard argument types. The command is listed in bold type. Words in italics are values that need to be specified by the user, and words in standard text are keywords to specify an option (which may or may not be followed by a value).
In the specification of the commands, arguments in []'s are optional and | represents "or". Arguments not in []'s are required.

ptraj input/output commands

ptraj commands which modify the ``state''

ptraj ``action'' commands

The following are commands that involve an action performed on each coordinate set as it is read in. The commands are listed in alphabetical order. Note that in the script the commands are applied in the order specified and some may change the overall state (more on this later). All of the actions can be applied repeatedly.

ptraj ``analzye'' commands

These commands are used to analyze any accumulated data on the scalarStack. This is usually done by reference to the name specified in commands such as distance, angle, etc. This code is currently under development!!! Contact the author for recent information...
thomas <>

Last modified: Mon May 3 15:43:39 EDT 1999