* This directory contains the force field files.

* Force field: GROMOS 54A7

* Format compatible with GROMACS >= 5

* 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) 
  - 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).
  - CTX : C-terminus protonated in all possible positions (according to
    tautomeric forms being considered) and parameters of _charged_ form.

    Note 1: Using NH3+ from regular distribution is ok because it has
    all protons needed. These special blocks for the N-terminus may be
    removed in the future.

    Note 2: It would be nicer to use more helpful names for the
    "extended" forms of the titrable residues, such as GLUX, LYSX,
    etc, or XGLU, XLYS, etc. However, pdb2gmx drasticaly limits the
    possible name choices because it insists on trying to guess and
    use instead the "proper" names for the residues (e.g., LYSX and
    XLYS are replaced by LYS). The currently adopted choice (GLX, LYX,
    etc) works, but it may break in the future if pdb2gmx is made even
    "smarter".

* Additional file protstates.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. Unchanged: forcefield.itp, ffnonbonded.itp, atomtypes.atp,
  aminoacids.r2b, aminoacids.vsd, dppc.itp, ff_dum.itp, ions.itp,
  popc.itp, spce.itp, spc.itp, tip3p.itp, tip4p.itp, tmcl.itp,
  watermodels.dat
  2. <FF>/ffbonded.itp : defined ga_CtrHH (ASX,GLX,TYX,CTX), gd_CtrCCOH
  (ASX,GLX,CTX), ga_SHH (CYX)
  3. residuetypes.dat, <FF>/aminoacids.rtp, <FF>/aminoacids.hdb : new
  building blocks are added accordingly (ASX, GLX, HIX, LYX, CYX, TYX)
  4. <FF>/aminoacids.n.tdb, <FF>/aminoacids.c.tdb : new termini are
  added accordingly (CTX, NTX, GLY-NTX, PRO-NTX)
  5. <FF>/protstates.dic : new file with state-dependent parameters for the new
  building blocks and termini
  