* This directory contains the force field files.

* Force field: GROMOS 54A7

* Additional building blocks for titrating residues (.rtp; .hdb;
  aminoacids.dat)
  - ASX : ASP protonated in all possible positions (according to
    tautomeric forms being considered) and parameters of tautomer 0.
  - GLX : the same for GLU.
  - HIX : the same for HIS.
  - LYX : the same for LYS.
  - CYX : the same for CYS.
  - TYX : the same for TYR.

  and titrating termini (.tdb) 
  - CTX : the same for C-terminus.
  - NTX : the same for N-terminus.
  - GLY-NTX : the same for N-terminus (GLY special case).
  - PRO-NTX : the same for N-terminus (PRO special case).

* Additional file ffG54a7pHt.dic: the DICTIONARY.  
This file contains the list of parameters that vary depending on the
state (tautomeric form) of each titrating residue.

      FORMAT

      1st field: residue name

      2nd field: parameter type, one of the following letters
    	   	 - q : charge
	   	 - t : atom type  
	   	 - b : bond
	   	 - a : angle
	   	 - d : dihedral (absent in this .dic because dihedrals
          	 don't change with state)
	   	 - i : improper (absent in this .dic because improper
              	 don't change with state)

      starting on 3rd field: atom names (one atom for "q" or "t"; two
      atoms for "b"; three atoms for "a"; four atoms for "d" or "i")

      after the atom names: number of states

      last fields: parameter (q|t|b|a|d|i) macros or values for each state 

      E.g. 

      1)

      TYR q CZ 3  0.20300  0.20300  -0.20000

      The charge of CZ in TYR in each of the 3 states: 0.20300 (state 0),
      0.20300 (state 1), -0.20000 (state 2)

      2)

      ASP t OD1 5  OA  O  OA  O  OM

      The atom type of OD1 in ASP in each of the 5 states: OA (state 0), O
      (state 1), OA (state 2), O (state 3), OM (state 4)

      3)

      GLU a CG CD OE1 5  ga_19  ga_30  ga_19  ga_30  ga_22

      The angle parameters of CG-CD-OE1 in GLU in all 5 states: ga_19 (state
      0), ga_30 (state 1), ga_19 (state 2), ga_30 (state 3), ga_22 (state 4)

      4)
      
      GLU a CG CD OE1 5  115.00 610.00  121.00 685.00  115.00 610.00  121.00 685.00  117.00      635.00

      Although not using macros, this line is exactly equivalent to the
      previous one for the GROMOS 54A7 force field. The same parameter form
      (macro or non-macro) must be used for each line, but different lines
      may use different forms.

* Differences regarding regular distribution (gromacs; in-house) files:

  1. specbond.dat, <FF>nb.itp, <FF>.atp : unchanged
  2. <FF>.itp : the names of files are changed accordingly
  3. <FF>bon.itp : defined ga_CtrHH (ASX,GLX,TYX,CTX), gd_CTrCCOH
  (ASX,GLX,CTX), ga_SHH (CYX)
  4. aminoacids.dat, <FF>.rtp, <FF>.hdb : new building blocks are
  added accordingly (ASX, GLX, HIX, LYX, CYX, TYX)
  5. <FF>-n.tdb, <FF>-c.tdb : new termini are added accordingly
  (CTX, NTX, GLY-NTX, PRO-NTX)
  6. <FF>.dic : new file with state-dependent parameters for the new
  building blocks and termini

