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Software: ptraj/rdparm

ptraj/rdparm is a program written in C that has two functions.

rdparm reads in AMBER prmtop files and allows users to inspect the stored information (see rdparm.html).

ptraj is a program for processing AMBER, CHARMM, and PDB trajectory files. It can convert trajectories, calculate bond, angles, dihedrals, RMSd value, mean-squared displacements, atomic positional fluctuations, order parameters/correlation functions, imaging of trajectories to various unit cells, etc.. A limited snapshot of the documentation is in ptraj.html.

Although ptraj is distributed within AMBER as part of the free set of "Amber Tools" (see Please let us know if you find bugs or add features of general use...

Development Snapshot:

Here is a link to a gzip'ed tar file of the current standalone source code: ptraj-9.9h.tar.gz (4 April 2008). Check back for updates!

Here is a link to a compressed tar file of the previous
standalone source code: ptraj-6.5.tar.Z
(25 June 2003).

Files are also available individually in this directory...

Note: new source code update as of 25 June 2003 fixes more bugs. See the file README.UPDATES for more information. This version properly handles DOS formatted prmtop files and more correctly handles X-PLOR PSF files. Imaging can be done to other unit cells with the xoffset, yoffset and zoffset commands (which may be useful for building up PDB files to show packing of unit cells)... More changes should come in time.

In the previous version, a long-standing (and ADDITIONAL) bug with the B-factors is fixed. B-factors are the positional fluctuations SQUARED multiplied by 8pi**2 (not the sqrt() as I mistakening posted on the AMBER e-mail reflector; whoops?). Other than this, the most useful addition is a new command to randomly swap solvent and ion positions to randomize initial ion placement and fixes in supporting AMBER7 prmtop files.

Force fields:

Note: for up-to-date versions of CHARMM compatible files for the newer force fields such as ff99SB and parmbsc0, please see Jeff Klauda's WWW page at U Maryland

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Last modified: Sometime in the year 2000