AMBER95 FORCE FIELD

			NOTES
                       -------------------------------------------------------------
1-4 scaling factor	The default 1-4 scaling factor is 0.5 for Amber forcefiled.
			In amber95 forcefield, the scaling factor is 0.5 for van der
			Waals interactions and 1/1.2 for electrostatic interactions.
			The scaling factor can be reset by the following command in
			discover_3 input file:
	
      			     forcefield scale \
          			vdw_1_4 = 0.5 \

          			coulomb_1_4 = 0.83333 

Improper torsion    	Improper torsion angle in orginal AMBER is defined in their 
			residule library by atom names.  Biosym residule library does 
			not provide this information.  Therefore, the improper torsion 
			angle is defined according to the parameters in the .frc file.  
			As a consequence, the orginal AMBER and Biosym AMBERT might 
			give slightly different improper torsion energies.  However, 
			this should not affect the simulation result in most cases.



reslib.tcl: 		Tcl script converts orginal AMBER residue library to Biosym 
			residue library using the existing Biosym residue library 
			(amber95.rlb) as a reference.

			If the number of atoms and name of each atom of the residue 
			in AMBER residue library file matches with one of the existing 
			residue in Biosym residue library (amber95.rlb), the existing 
			residue will be updated with the new atom types, atomic partial 
			charges, and out-of-plane flags by AMBER residue library.  If 
			the residue is not found in the existing amber95.frc, a new residue
			will be created with correct atom type, partial charge, connectivity,
			and out-of-plane flag.  Other informations such as charge group, 
			switching atom, and torsion angles will be ignored.  

			To run the script:
			1. Check out amber95.frc and put amber residue library file 
			  in your local directory.
			2. Run discover_3 with the following input file.
   			3. The new residule library is called my_amber95.rlb.  

			#BIOSYM dsl 3
			#
			source $BIOSYM/gifts/fdiscover/reslib.tcl
			reslib AMBER_residue_library_file amber95


   
frc.tcl: 		Tcl script Creates new .frc file from AMBER parameter file 
			(parm94.dat).  

			The element type listed in atom_type table in .frc file generated
			by this script is the first character of the atom type listed in 
			AMBER parameter file.  They might be wrong.  However they are not
			used in any calculation.

			To run the script:
			1. Put amber parameter file in your local directory.
			2. Run discover_3 with the following input file.
			3. The file created is my_amber95.frc.  

                        #BIOSYM dsl 3
                        #
                        source $BIOSYM/gifts/fdiscover/frc.tcl
                        frc AMBER_parameter_file (replace this with your amber 
			parameter file name)
