_______________________________________________________________________

      README.UPDATES:

           This file describes the latest released 
          modifications to the ptraj/rdparm programs

     e-mail me if you have problems: cheatham@chpc.utah.edu
_______________________________________________________________________

25 June 2003: VERSION 6.5

-- Fixed a bug in reading XPLOR PSF files

-- Fixed a problem in reading DOS format prmtop files that end a 
   line with \r\n rather than simply \n

-- Added a command to count the atoms in a particular selection in rdparm

-- Changed the logic on the appended set number for PDB files such
   that the number is only incremented for valid coordinate sets.

-- increased the density of the plot schematic for the hydrogen bond
   lifetimes

-- fixed a bug in the RDF related to determining the number of bins

-- added an offset to the imaging command to allow imaging to other
   than the central unit cell, i.e. image xoffset 1 images to the unit
   cell one box over in the x-direction.



10 June 2002: VERSION 6.4

-- Fixed a bug reading new style AMBER7 prmtop's when there are no
   angle or dihedral terms.

-- Fixed another and BIG long-standing bug in the B-factor code.
   B-factors are not simply the atomic fluctuations multiplied by
   8pi**2 but the fluctuations SQUARED multiplied by this factor.  Whoops.

-- randomizeions command added: Swaps positions of solvent and ions
   randomly keeping minimum overlap between solute/ions as specified.

-- documented the checkoverlap command; this command looks for
   minimum/maximum distance violations.  Also added the "around"
   keyword to look for violations of atoms to a particular subset of
   atoms (i.e. ions around the DNA).

-- modified the h-bond code to print out a pseudo-time series
   schematic in the output to track "when" the bonds occur.

-- Fixed bug with reading NEW amber7 format prmtop files


16 October 2001: VERSION 6.3

-- fixed long standing bug in the bfactor (atomicfluct) routine that
   incorrectly multiplied the bfactor value twice when accumulating
   byres or mymask

-- added support for new prmtop format (Case) of AMBER 7

5  September 2001: VERSION 6.2

-- Added printDelphi command to rdparm to dump out the charges for the
   current prmtop in a format that (academic) Delphi expects

-- added the "echo" command to ptraj which will simply print out the
   line of text (into the output) that follows the echo.  This is
   useful for adding comments, etc.

-- fixed the printAtom command to not dump core on CHARMM PSF's.
   Still need to add code to print out atom info for PSF's however...

-- fixed the parsing of the diffusion time between frames to be
   non-integer

-- fixed a big bug in the principal axis code.  Still trying to
   resolve issues with flipping eigenvalues, etc.

13 July 2001:

-- added the "checkoverlap" command to ptraj.
   checkoverlap [mask] [min <value>] [max <value>] [noimage] 
   This will look through the list of atoms to look for atoms that
   have distances less than the specified minimum value (0.95) or
   greater than the maximum value (if specified).  You can turn off
   imaging with the noimage keyword

-- minor fixes in printing and fixed some memory leaks


7  November 2000:

-- fixed problem with "average" command and dumping of coordinates.
   When only a subset of the atoms were selected the wrong coordinates
   were being dumped unless the selection was sequential starting from
   the first atom.


31 October 2000:

-- added a command to rdparm to "printdelphicharge", i.e. a file of
   charges for the current parmtop that is in the format required by
   the Delphi program to assign charges.

-- fixed up the printing of hydrogen bond information; modified the
   h-bond command to not include "self" (within residue) h-bonds
   unless requested.

-- removed references to <strings.h> and replaced with <string.h>


7  September 2000:

-- turned off the automatic imaging of distances if no box angles
   are specified

-- fixed the handing of .gz and .Z files; allows the creation of
   compressed output trajectories on the fly (via the specification of
   .gz or .Z in the trajout filename)

-- fixed the semantics of "go"

-- fixed a bad memory problem when reading CHARMM trajectories

-- fixed the image familiar command to work properly.