--- /dev/null
+ 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
projects / unres.git / blobdiff