//
// Definition file for titratable residues
//
// Jens Erik Nielsen, University College Dublin 2004
//
// ---------------------------------------------------
//
// This file decides which residues are titratable and which aren't
// All transitions that will be calculated, must be included in this file
//
// If a particular residue type has more than one transition, then these other transitions
// must be stated explicitly. 
//
// The format for a single transition is the following:
// * <Transition name>                                # Start of record, name of this transition
// Residue: <Residue identifier>                      # The residue type that this transition is associated with
//                                                    # Simply the residue name or NTR, CTR, PNTR (proline Nterm)
// Grouptype: <type>                                  # Acid or Base
// Transition: <state #s start> -> <state #s end>     # Indicate the identifier of the states as
//                                                    # given in HYDROGENS.DAT. If one of the states
//                                                    # is 0 hyds, then give the state no. for that state
//                                                    # is 0. Several state nums are separated with commas.
// Model pKa: <model pKa value for above transition>
// # If more transitions are needed then these are simply stated below the first two
// [Transition: start: <state #s start> end: <state #s end>
// [Model pKa: <model pKa value for above transition>]
// END                                           # Record ends
// END OF FILE                                   # File ends
// Model pKa adjusted for four neutral states (cis/trans energy difference accounted for)
* ASP
Residue: ASP
Grouptype: Acid
//Transition: 1,2,3,4 -> 0
Transition: ASH1c,ASH1t,ASH2c,ASH2t -> ASP
Model_pKa: 3.9
END

// *Carboxylic_Acid
// Residue: UNKNOWN
// Grouptype: Acid
// Transition: 1 -> 0
// Model_pKa: 0.0
// END 
// Model pKa adjust for four neutral states (cis/trans energy difference accounted for)
* GLU
Residue: GLU
Grouptype: Acid
//Transition: 1,2,3,4 -> 0
Transition: GLH1c,GLH1t,GLH2c,GLH2t -> GLU
Model_pKa: 4.1
END

* ARG
Residue: ARG
Grouptype: Base
//Transition: 1+2+3+4 -> 1+2+3+4+5 
Transition: ARG0 -> ARG
Model_pKa: 13.0
END

* LYS
Residue: LYS
Grouptype: Base
//Transition: 1 -> 0
Transition: LYS -> LYS0
Model_pKa: 10.4
END 

* TYR
Residue: TYR
Grouptype: Acid
//Transition: 1 -> 0
Transition: TYR -> TYR-
Model_pKa: 9.6
END 

// Model pKa adjusted for two neutral states
* HIS
Residue: HIS
Grouptype: Base
//Transition: 1,2->1+2
Transition: HSD,HSE->HSP
Model_pKa: 6.6
END 

// Model pKa adjusted for two neutral states
* NTR
Residue: All
Grouptype: Base
//Transition: 1,2->1+2
Transition: H3,H2 -> H3+H2
Model_pKa: 8.3
END

// Model pKa adjusted for four neutral states
* CTR
Residue: All
Grouptype: Acid
//Transition: 1,2,3,4 -> 0
Transition: CTR01c,CTR01t,CTR02c,CTR02t -> CTR-
Model_pKa: 3.2
END

END OF FILE

