Software, benchmarks, ...

Software: ptraj/rdparm

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!

• Note that this is an interim / development pre-release!!! Use at own risk!!! Note also that this may be barely more up-to-date than the Amber Tools release!

  This is a snapshot of what is available in Amber Tools within AMBER 10. This includes updates to the atom selection parser to be compatible with AMBER, addition of the ability to cluster MD trajectories, and other significant changes. The standalone version now includes support for all of the matrix functionality. The documentation is not complete; please refer to the comments in the code and previous documentation. Additional preliminary information on the clustering is here in this PDF file; see also our clustering paper:

  J. Shao, S. W. Tanner, N. Thompson, T.E. Cheatham, III. "Clustering molecular dynamics trajectories: I. Characterizing the performance of different clustering algorithms." J. Chem. Theory Comp. 3, 2312-2334 (2007).
       [ local PDF: ACS Link + Supporting info ]

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:

• Cornell et al. force field within CHARMM.
  cornell_all.rtf (residue/topology file)
  cornell_all.prm (parameters)
  cornell_na.rtf (residue/topology file for nucleic acids)
  cornell_na.prm (parameters for nucleic acids only)<

• The parm98.dat nucleic acid force field in AMBER. This improves sugar pucker phases and glycosidic torsion (chi) values for B-DNA in Cornell et al. (at the expense of A-DNA stabilization in mixed water/ethanol solutions and B-DNA to A-DNA transitions with hexaammine-cobalt(III).
  parm98.dat

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