OPUS-Rota v1.0 
Copyright (c) 2008 Minygang Lu and Jianpeng Ma.  All rights reserved.

REFERENCE:
OPUS-Rota: A Fast and Accurate Method for Side-chain Modeling. Mingyang Lu, 
Athanasios D. Dousis and Jianpeng Ma, Protein Science (2008), in press.

USAGE:
batch mode:
% ./opus_rota

usage notes:
1. This version supports only side-chain modeling of the whole protein.
2. All parameters are in "config.rota".  The important parameters are:
   a. energy_dir : the directory of energy data
   b. filelist : the list file of input structures
   c. out_dir : the directory for storing output files 
      (the output files have the same prefix as the input files but 
      end with ".out")
3. In the energy data directory (energy_dir), another executable "make_lib" 
   is provided to convert Dunbrack's backbone-dependent rotamer library 
   into the smaller binary file used in OPUS-Rota.  In this package, the 
   converted binary library file is alreay provided using 
   "./make_lib bbdep02.May.sortlib"
4. This software has been compiled and tested for Ubuntu x86 Linux.
