;;;;;; AMINO ACIDS -- VERSION 2.2P 
;
; S.J. Marrink, 16-06-2008.
;
; version 04-07-2012 - changed BAS to BB, SID to SC1, DdJ.
; version 2.2P, 05-12-2012, update by DdJ
; version 22-9-2010 - fix in charge group numbers for TRP
;
; To generate a complete protein topology, use the martinize.py script.
;
; please cite:
;
; D.H. de Jong, G. Singh, W.F.D. Bennet, C. Arnarez, T.A. Wassenaar, L.V. Schafer,
; X. Periole, D.P. Tieleman, S.J. Marrink.
; Improved Parameters for the Martini Coarse-Grained Protein Force Field
; J. Chem. Theory Comput., DOI: 10.1021/ct300646g
;
; &
;
; L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D.P. Tieleman, S.J. Marrink.
; The MARTINI forcefield: Extension to peptides and proteins.
; J. Chem. Th. Comp., 4:819-834, 2008.
;
;
; BACKBONE
; the backbone of the amino acids consist of one particle, which represents
; the center-of-mass of the NH2-Calpha-C=O unit. 
; For a single aminoacid, the backbone is very polar
; and is represented by a "P5" particle.

; However: as part of a secondary structure element inside a peptide or
; protein a particle type of reduced polarity should be used. For details
; see the original publications.

; SIDECHAIN GEOMETRY
; most amino acids except GLY and ALA have at least one site representing
; the side chain. The backbone-sidechain distance was estimated from 
; the underlying atomistic structure and thus reflects the size of the 
; amino acid quite accurately. Most side chains are attached to the
; backbone with weak bonds to mimic flexibility of the underlying structure.
; A few attachments are stiffer and are modeled by constraints.


;;; GLYCINE

[ moleculetype ]
; molname       nrexcl
GLY                1			

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     GLY    BB     1      0      


;;; ALANINE

[ moleculetype ]
; molname       nrexcl
ALA                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P4    1     ALA    BB     1      0     ; ALA slightly less polar 


;;; CYSTEINE

[ moleculetype ]
; molname       nrexcl
CYS                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     1   CYS    BB     1      0
 2   C5     1   CYS    SC1    2      0     

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.31     7500        


;;; VALINE

[ moleculetype ]
; molname       nrexcl
VAL                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     VAL     BB     1      0    
 2   C2   1     VAL     SC1    2      0    

[constraints]
;  i     j   funct   length  
   1     2    1       0.265       


;;; LEUCINE

[ moleculetype ]
; molname       nrexcl
LEU                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     LEU     BB     1      0    
 2   C1   1     LEU     SC1    2      0    

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.33     7500    


;;; ISOLEUCINE

[ moleculetype ]
; molname       nrexcl
ILE                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     ILE     BB     1      0    
 2   C1   1     ILE     SC1    2      0    

[constraints]
;  i     j   funct   length  
   1     2    1       0.31       


;;; METHIONINE

[ moleculetype ]
; molname       nrexcl
MET                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     MET     BB     1      0    
 2   C5   1     MET     SC1    2      0     

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.40     2500


;;; PROLINE

[ moleculetype ]
; molname       nrexcl
PRO                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     PRO     BB     1      0    
 2   C3   1     PRO     SC1    2      0    

[bonds]
;  i     j   funct   length  force.c.
  1     2    1       0.30     7500


;;; ASPARAGINE

[ moleculetype ]
; molname       nrexcl
ASN                1

[ atoms ]
;id type resnr residu atom cgnr   charge  mass
 1   P5    1     ASN     BB     1      0  72
 2   Nda   1     ASN     SC1    2      0  0 
 3   D     1     ASN     SC2    3  +0.46  36
 4   D     1     ASN     SC3    4  -0.46  36

[virtual_sites2]
; Site from       funct a
   2     3    4   1     0.5

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.32     5000

[constraints]
;  i     j   funct   length 
   3     4    1       0.28   

;;; GLUTAMINE

[ moleculetype ]
; molname       nrexcl
GLN                1

[ atoms ]
;id type resnr residu atom cgnr   charge  mass
 1   P5    1     GLN     BB     1      0  72
 2   Nda   1     GLN     SC1    2      0  0
 3   D     1     GLN     SC2    3  +0.46  36
 4   D     1     GLN     SC3    4  -0.46  36

[virtual_sites2]
; Site from       funct a
   2     3    4   1     0.5

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.40     5000     

[constraints]
;  i     j   funct   length 
   3     4    1       0.28   

;;; ASPARTATE

[ moleculetype ]
; molname       nrexcl
ASP                1

[ atoms ]
;id type resnr residu atom cgnr   charge  mass
 1   P5     1     ASP     BB     1     0  72
 2   Qa     1     ASP     SC1    2     0  36
 3   D      1     ASP     SC2    3  -1.0  36

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.32     7500

[constraints]
;  i     j   funct   length 
   2     3    1       0.11   

;;; ASPARTATE - NEUTRAL FORM

[ moleculetype ]
; molname       nrexcl
ASP0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     1     ASP0    BB     1      0    
 2   P3     1     ASP0    SC1    2      0    

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.32     7500


;;; GLUTAMATE

[ moleculetype ]
; molname       nrexcl
GLU                1

[ atoms ]
;id type resnr residu atom cgnr   charge mass
 1   P5     1     GLU     BB     1     0 72 
 2   Qa     1     GLU     SC1    2     0 36 
 3   D      1     GLU     SC2    3  -1.0 36 

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.40     5000     

[constraints]
;  i     j   funct   length 
   2     3    1       0.11   

;;; GLUTAMATE - NEUTRAl FORM

[ moleculetype ]
; molname       nrexcl
GLU0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     1     GLU0    BB     1      0    
 2   P1     1     GLU0    SC1    2      0    

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.40     5000    


;;; THREONINE

[ moleculetype ]
; molname       nrexcl
THR                1

[ atoms ]
;id type resnr residu atom cgnr   charge    mass
1   P5     1     THR     BB     1      0    72
2   Nda    1     THR     SC1    2      0    0
3   D      1     THR     SC2    3  +0.31    36
4   D      1     THR     SC3    4  -0.31    36

[virtual_sites2]
; Site from       funct a
   2     3    4   1     0.5

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.26     9000

[constraints]
;  i     j   funct   length 
   3     4    1       0.28   

;;; SERINE

[ moleculetype ]
; molname       nrexcl
SER                1

[ atoms ]
;id type resnr residu atom cgnr   charge    mass
1   P5     1    SER     BB     1      0     72
2   N0     1    SER     SC1    2      0     0
3   D      1    SER     SC2    3  +0.40     36
4   D      1    SER     SC3    4  -0.40     36

[virtual_sites2]
; Site from       funct a
   2     3    4   1     0.5

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.25     7500

[constraints]
;  i     j   funct   length 
   3     4    1       0.28   

;;; LYSCNE 

[ moleculetype ]
; molname       nrexcl
LYS                1

[ atoms ]
;id type resnr residu atom cgnr   charge  mass
 1   P5    1     LYS     BB     1      0  72
 2   C3    1     LYS     SC1    2      0  72
 3   Qd    1     LYS     SC2    3      0  36
 4   D     1     LYS     SC3    4    1.0  36

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.33     5000      
   2     3    1       0.28     5000  

[constraints]
;  i     j   funct   length 
   3     4    1       0.11   

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   180.000    25.0      


;;; LYSCNE - NEUTRAL FORM

[ moleculetype ]
; molname       nrexcl
LYS0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5    1     LYS     BB     1      0    
 2   C3    1     LYS     SC1    2      0    
 3   P1    1     LYS     SC2    3      0    

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.33     5000      
   2     3    1       0.28     5000  

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   180.000    25.0      


;;; ARGININE 

[ moleculetype ]
; molname       nrexcl
ARG                1

[ atoms ]
;id type resnr residu atom cgnr   charge  mass
1   P5     1     ARG     BB     1      0  72
2   N0     1     ARG     SC1    2      0  72
3   Qd     1     ARG     SC2    3      0  36
4   D      1     ARG     SC3    4    1.0  36

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.33     5000   
   2     3    1       0.34     5000  

[constraints]
;  i     j   funct   length 
   3     4    1       0.11   

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   180.000    25.0      


;; ARGININE - NEUTRAL FORM

[ moleculetype ]
; molname       nrexcl
ARG0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     ARG0    BB     1      0    
2   N0     1     ARG0    SC1    2      0    
3   P4     1     ARG0    SC2    3      0    

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.33     5000       
   2     3    1       0.34     5000     

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   180.000    25.0      


;;; HISTIDINE 

[ moleculetype ]
;molname       nrexcl
HIS                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     HIS     BB     1      0    
2   SC4    1     HIS     SC1    2    0    ; three side chains in triangle
3   SP1    1     HIS     SC2    3    0    ; configuration, mimicking
4   SP1    1     HIS     SC3    4    0    ; ring structure

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.32     7500 

[constraints]
;  i     j   funct   length  
   2     3    1       0.27    
   2     4    1       0.27   
   3     4    1       0.27  

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   150.000   50.0  
    1     2    4       2   150.000   50.0 

[dihedrals]
;  i     j    k    l   funct   angle  force.c.
   1     3    4    2       2    0.0    50.0     ; to prevent backflipping of ring

;;; HISTIDINE, charged.

[ moleculetype ]
;molname       nrexcl
HISH               1

[ atoms ]
;id type resnr residu atom cgnr   charge  mass
1   P5     1     HIS     BB     1    0    72
2   SC4    1     HIS     SC1    2    0    72 ; three side chains in triangle
3   SP1    1     HIS     SC2    3    0    72 ; configuration, mimicking
4   SQd    1     HIS     SC3    4    0    36 ; ring structure
5   D      1     HIS     SC4    5  1.0    36

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.32     7500 

[constraints]
;  i     j   funct   length  
   2     3    1       0.27    
   2     4    1       0.27   
   3     4    1       0.27  
   4     5    1       0.11  

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   150.000   50.0  
    1     2    4       2   150.000   50.0 

[dihedrals]
;  i     j    k    l   funct   angle  force.c.
   1     3    4    2       2    0.0    50.0     ; to prevent backflipping of ring


;;; PHENYLALANINE

[ moleculetype ]
; molname       nrexcl
PHE                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     PHE     BB     1    0
2   SC5    1     PHE     SC1    2    0    ; three side chains in triangle
3   SC5    1     PHE     SC2    3    0    ; configuration, mimicking
4   SC5    1     PHE     SC3    4    0    ; ring structure

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.31     7500 	

[constraints]
;  i     j   funct   length  
   2     3    1       0.27     
   2     4    1       0.27    
   3     4    1       0.27   

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   150.000   50.0  
    1     2    4       2   150.000   50.0 

[dihedrals]
;  i     j    k    l   funct   angle  force.c.
   1     3    4    2       2    0.0    50.0     ; to prevent backflipping of ring


;;; TYROSCNE

[ moleculetype ]
; molname       nrexcl
TYR                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     TYR     BB     1    0
2   SC4    1     TYR     SC1    2    0  
3   SC4    1     TYR     SC2    3    0 
4   SP1    1     TYR     SC3    4    0  

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.32     5000 	

[constraints]
;  i     j   funct   length  
   2     3    1       0.27     
   2     4    1       0.27    
   3     4    1       0.27   

[angles]
;  i     j    k     funct   angle  force.c.
    1     2    3       2   150.000   50.0  
    1     2    4       2   150.000   50.0 

[dihedrals]
;  i     j    k    l   funct   angle  force.c.
   1     3    4    2       2    0.0    50.0     ; to prevent backflipping of ring


;;; TRYPTOPHAN

[ moleculetype ]
;molname       nrexcl
TRP                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5       1     TRP     BB     1    0
2   SC4      1     TRP     SC1    2    0    
3   SNd      1     TRP     SC2    3    0
4   SC5      1     TRP     SC3    4    0
5   SC5      1     TRP     SC4    5    0

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.30     5000 	

[constraints]
;  i     j   funct   length  
   2     3    1       0.27     
   3     4    1       0.27    
   2     4    1       0.27   
   3     5    1       0.27    
   4     5    1       0.27   

[angles]
;  i     j    k     funct   angle  force.c.
   1     2    3       2   210.000   50.0 
   1     2    4       2   90.000    50.0  

[dihedrals]
;  i     j    k    l   funct   angle  force.c.
   1     3    4    2       2    0.0    50.0     ; to prevent backflipping of ring
   2     3    5    4       2    0.0    200.0    ; to keep plane fixed



