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      modeling Loops of Proteins by Simulated Annealing method

		     WRITTEN BY DR. HONGYU ZHANG

		     CARB, University of Maryland

		  	   August, 1998 		      

			   VERSION 1.0b

============================================================================

This is a short introduction to protein loops modeling program LPSA. For 
theory, please refer "A Fast and Efficient Program for Modeling Protein loops", 
Zhang H., Lai L., Wang L., Han Y. and Tang Y.  Biopolymers, Vol.41, P61-72, 
1997 

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Major revision to Version 1.0a.

. After setting up a big MAXATOM number, the excutable code can be used to 
  model different proteins without re-compiling.


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Directory src/ contains the C++ code of LPSA. An example of BPTI loop 
modeling is in directory example/.

The I/O file of LPSA is as follows,

INNAME
The input PDB coordinates of both protein atoms and loop atoms, where the
protein atoms is in the same positions as in crystal structure while loop 
segment is in strech conformation.

RANDOM
Random seeds of Monte-Carlo algorithm.

LOOPSE
Start and End residue positions of protein loop segment; the Conformational 
Search Number of Each Cycle (CSNEC).

TORTEMP
Template to generate the topology of torsion angles of each of 20 amino 
acid residues.

GRID_PARA
Parameter file for grid-mapping method. It is generated in the first run of
LPSA, and then can be read in the following runs, which will save us from
regenerating this file.

=========================================================================

This program is free to use and distribute. If either the program or 
ideas from its code are used in a publication, it is asked that the 
following reference be cited:

"A Fast and Efficient Program for Modeling Protein loops",
Zhang H., Lai L., Wang L., Han Y. and Tang Y.  
Biopolymers, Vol.41, P61-72, 1997


For any questions, bugs or comments, please contact
hyzhang@carb.nist.gov or
