XDRF2PDB, XDRF2PDB-M, XDRF2X - programs to convert compressed 
          Cartesian coordinate files from UNRES into ASCII formats
          ------------------------------------------------------------

TABLE OF CONTENTS
-----------------

1. License terms

2. Programs and their functions

3. Installation

4. Command lines and files
   4.1 xdrf2pdb
   4.2 xdrf2pdb-m
   4.3 xdrf2x
   4.4 xdrf2ang

5. Support

1. LICENSE TERMS
----------------

* This software is provided free of charge to academic users, subject to the
  condition that no part of it be sold or used otherwise for commercial
  purposes, including, but not limited to its incorporation into commercial
  software packages, without written consent from the authors. For permission
  contact Prof. H. A. Scheraga, Cornell University.

* This software package is provided on an "as is" basis. We in no way warrant
  either this software or results it may produce.

* Reports or publications using this software package must contain an
  acknowledgment to the authors and the NIH Resource in the form commonly
used
  in academic research.

2. PROGRAMS AND THEIR FUNCTONS
------------------------------

The following three programs can be used to extract conformations from
compressed Cartesian (cx) files from UNRES:

xdrf2pdb - takes a single trajectory file and converts it into PDB format.

xdrf2pdb-m - takes a multiple-trajectory file from UNRES/MREMD simulations
           and enables the user to extract conformation of a particular 
           trajectory and save them to a PDB file.

xdrf2x - takes a single trajectory file and converts it into UNRES Cartesian
           coordinate (x) format

xdrf2ang - takes a single trajectory file and calculates UNRES backbone 
         angles (theta and gamma).

3. INSTALLATION
---------------

Run make all on your system to install all programs or make <program> 
to install a particular program. You might need to run make in the 
xdrf subdirectory beforehand or point to the xdrf library that is on another
directory in the Makefile.

The program compiles on all known Fortran compilers, including gfortran.

4. COMMAND LINE AND FILES
-------------------------

For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file 
in either one- or three-letter code.

4.1 XDRF2PDB

Command line syntax:

xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]

where 

one or three indicates in what format the sequence will be read

seqfile - the file with the sequence:

one-letter format: 80A1

three-letter format: 20(A3,1X)

Note that the sequence must match exactly the UNRES sequence 

cxfile - full name of the trajectory file with compressed Cartesian coordinates.

freq (1) - conformation sampling frequency (each freq-th conformation will
        be saved to PBD file

start (1)  - the first conformation to be saved to PDB file

end (1000000000) the last conformation to be saved to PDB file

pdbfile (cxfile with extension changed from cx to pdb) - the output PDB file

4.2 XDRF2PDB-M

Command line syntax:
xdrf2pdb-m xdrf2pdb-m one/three seqfile cxfile ntraj itraj [pdbfile] [freq]

cxfile - the name of the compressed trajectory file from an UNRES/MREMD run
         carried out with TRAJ1FILE (conformations from all trajectories
         output to a single file)
      
ntraj - number of trajectories in the multi-trajectory run

itraj - the number of trajectory to be extracted

pdbfile - (cxfile-without-cx-itraj.pdb) the name of file to write the Cartesian 
        coordinates of trajectory itraj to

freq (1) - output frequency

The xdrf2pdb program to convert cx files to pdb files

The source is in xdrf2pdb; it requires the libraries in xdrf

4.3 XDRF2X

Command line syntax:

xdrf2x cxfile [is] [ie] [freq] > x_file

The meaning of the the arguments is as in section 4.1; the conformations
are output in UNRES Cartesian coordinate format to stdout.

4.4. XDRF2ANG

Command line syntax:

xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile]

The meaning of the first six parameters is as in section 4.1; angfile is
the name of the output angle file; is assigned cx file name with the cx 
extension changed to ang, if not present.

5. SUPPORT
----------

   Dr. Adam Liwo
   Faculty of Chemistry, University of Gdansk
   ul. Sobieskiego 18, 80-952 Gdansk Poland.
   phone: +48 58 523 5430
   fax: +48 58 523 5472
   e-mail: adam@chem.univ.gda.pl

   Dr. Cezary Czaplewski
   Faculty of Chemistry, University of Gdansk
   ul. Sobieskiego 18, 80-952 Gdansk Poland.
   phone: +48 58 523 5430
   fax: +48 58 523 5472
   e-mail: czarek@chem.univ.gda.pl

Prepared by Adam Liwo, 11/26/11