+++ /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