Cheatham Group

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..
ptraj is now freely distributed within AMBER as part of the free set of "Amber Tools" (see ambermd.org).

Please let us know if you find bugs or add features of general use...


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

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