martini_v2.2_aminoacids_lipidtails_ASG.itp

;;;;;; AMINO ACIDS -- VERSION 2.2 
;
; S.J. Marrink, 16-06-2008.
;
; version 2.2, 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 martinizi.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.
;----------------------------------------------------------------------------------------
;
;(1) Updated with lipid tail parameters according to DOI:10.1021/acs.jpcb.7b10175 - Dheeraj Prakaash - 02.Oct.2019
;     CYS Farnesyl 		= CYF
;     CYS Geranylgeranyl 	= CYG
;     CYS Palmitoyl		= CYP
;     N-terminal GLY Myristoyl	= GMN
;----------------------------------------------------------------------------------------
;(2) Updated with Asparagine glycosylation (ASG) parameters according to DOI:10.1021/acs.jcim.0c00495 - Dheeraj Prakaash - 24.Nov.2020
;----------------------------------------------------------------------------------------

;;; GLYCINE

[ moleculetype ]
; molname       nrexcl
GLY                1			

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


;;; ALANINE

[ moleculetype ]
; molname       nrexcl
ALA                1

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


;;; CYSTEINE

[ moleculetype ]
; molname       nrexcl
CYS                1

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

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


;;; CYSTEINE FARNESYL

[ moleculetype ]
; molname       nrexcl
CYF		1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     3   CYF    BAS    1      0
 2   C5     3   CYF    SI1    2      0
 3   C3	    3   CYF    SI2    3      0
 4   C3     3   CYF    SI3    4      0
 5   C3     3   CYF    SI4    5      0
 6   C3	    3   CYF    SI5    6      0
 
[ bonds ]
;   i   j   funct      length  force.c.
    1	2	1	0.39	8000
    2	3	1	0.42	6000
    3	4	1	0.43	5000
    4	5	1	0.31	12000
    5	6	1	0.23	15000
     
[ angles ]
; i     j       k     funct   angle  force.c. 
  1	2	3	2	180	65
  2	3	4	2	125	42
  3	4	5	2	130	48
  4	5	6	2	170	50


;;; CYSTEINE GERANYLGERANYL

[ moleculetype ]
; molname       nrexcl
CYG		1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     3   CYG    BAS    1      0
 2   C5     3   CYG    SI1    2      0
 3   C3	    3   CYG    SI2    3      0
 4   C3     3   CYG    SI3    4      0
 5   C3     3   CYG    SI4    5      0
 6   C3	    3   CYG    SI5    6      0
 7   C3	    3   CYG    SI6    7      0
 
[ bonds ]
;   i   j   funct      length  force.c.
    1	2	1	0.38	8500
    2	3	1	0.42	6000
    3	4	1	0.42	7750
    4	5	1	0.41	7000
    5	6	1	0.40	9000
    5	6	1	0.24	8000
     
[ angles ]
; i     j       k     funct   angle  force.c. 
  1	2	3	2	150	50
  2	3	4	2	125	55
  3	4	5	2	130	45
  4	5	6	2	180	38
  5     6       7       2	180 	75

;;; CYSTEINE PALMITOYL

[ moleculetype ]
; molname       nrexcl
CYP		1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     3   CYP    BAS    1      0
 2   C5     3   CYP    SI1    2      0
 3   C1	    3   CYP    SI2    3      0
 4   C1     3   CYP    SI3    4      0
 5   C1     3   CYP    SI4    5      0
 6   C1	    3   CYP    SI5    6      0
 
[ bonds ]
;   i   j   funct      length  force.c.
    1	2	1	0.38	8000
    2	3	1	0.39	5000
    3	4	1	0.47	4500
    4	5	1	0.47	4500
    5	6	1	0.41	5500
     
[ angles ]
; i     j       k     funct   angle  force.c. 
  1	2	3	2	150	35
  2	3	4	2	125	25
  3	4	5	2	180	25
  4	5	6	2	180	28


;;; GLYCINE MYRISTOYL (N-TERMINUS GLY ONLY)

[ moleculetype ]
; molname       nrexcl
GMN		1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   Nda    3   GMN    BAS    1      0
 2   C1     3   GMN    SI1    2      0
 3   C1	    3   GMN    SI2    3      0
 4   C1     3   GMN    SI3    4      0
 5   C1     3   GMN    SI4    5      0
 
[ bonds ]
;   i   j   funct      length  force.c.
    1	2	1	0.36	7500
    2	3	1	0.47	3000
    3	4	1	0.47	4000
    4	5	1	0.36	5000
     
[ angles ]
; i     j       k     funct   angle  force.c. 
  1	2	3	2	140	30
  2	3	4	2	160	38
  3	4	5	2	175	45


;;; VALINE

[ moleculetype ]
; molname       nrexcl
VAL                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5   1     VAL     BAS    1      0    
 2   AC2  1     VAL     SID    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     BAS    1      0    
 2   AC1  1     LEU     SID    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     BAS    1      0    
 2   AC1  1     ILE     SID    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     BAS    1      0    
 2   C5   1     MET     SID    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     BAS    1      0    
 2   C3   1     PRO     SID    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
 1   P5    1     ASN     BAS    1      0    
 2   P5    1     ASN     SID    2      0    

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


;#-------------------------------------------------------------------------------------------#
;;; ASPARAGINE Glycosylated (N-acetyl glucosamine Asparagine) - DOI:10.1021/acs.jcim.0c00495
;;; - Dheeraj Prakaash (Nov 2020)

[ moleculetype ]
; molname       nrexcl
ASG                1

;----structure----
;  P1
;   \
;   SP2--P5--P5
;   /
;  P3
;   \
;   SP1

[ atoms ]
;id type resnr residu   atom  cgnr   charge
 1   P5    1     ASG     BAS    1      0	; A1
 2   P5    1     ASG     SI1    2      0	; A2
 3   SP2   1     ASG     SI2    3      0	; G2
 4   P1    1     ASG     SI3    4      0	; G1
 5   P3    1     ASG     SI4    5      0	; G3
 6   SP1   1     ASG     SI5    6      0	; G4

[bonds]
;  i     j   funct   length  force.c.
   1     2    1       0.320     5000
   2     3    1       0.474    30000
   4     3    1       0.238    30000
   3     5    1       0.222    30000
   5     6    1       0.312    30000

[angles]
;  i     j    k     funct   angle  force.c.
   1     2    3       2    115.000   170.0
   4     3    2       2     45.000    50.0
   2	 3    5	      2     35.000   120.0
   4     3    5       2    135.000   300.0
   3     5    6       2    145.000   250.0

[dihedrals]
;  i     j    k    l   funct   angle  force.c.
   1     2    3    4       2    80.0     8.0   
   1     2    3    5       2   300.0     8.0    
   4     3    5    6       2   180.0    15.0
;#----------------------------------------------------------------------#

;;; GLUTAMINE

[ moleculetype ]
; molname       nrexcl
GLN                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5    1     GLN     BAS    1      0    
 2   P4    1     GLN     SID    2      0    

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


;;; ASPARTATE

[ moleculetype ]
; molname       nrexcl
ASP                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     1     ASP     BAS    1      0    
 2   Qa     1     ASP     SID    2   -1.0    

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


;;; ASPARTATE - NEUTRAL FORM

[ moleculetype ]
; molname       nrexcl
ASP0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     1     ASP0    BAS    1      0    
 2   P3     1     ASP0    SID    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
 1   P5     1     GLU     BAS    1      0    
 2   Qa     1     GLU     SID    2   -1.0    

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


;;; GLUTAMATE - NEUTRAl FORM

[ moleculetype ]
; molname       nrexcl
GLU0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5     1     GLU0    BAS    1      0    
 2   P1     1     GLU0    SID    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
1   P5     1     THR     BAS    1      0    
2   P1     1     THR     SID    2      0    

[constraints]
;  i     j   funct   length 
   1     2    1       0.26   


;;; SERINE

[ moleculetype ]
; molname       nrexcl
SER                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1    SER     BAS    1      0    
2   P1     1    SER     SID    2      0    

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


;;; LYSINE 

[ moleculetype ]
; molname       nrexcl
LYS                1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5    1     LYS     BAS    1      0    
 2   C3    1     LYS     SI1    2      0    
 3   Qd    1     LYS     SI2    3    1.0    

[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      


;;; LYSINE - NEUTRAL FORM

[ moleculetype ]
; molname       nrexcl
LYS0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
 1   P5    1     LYS     BAS    1      0    
 2   C3    1     LYS     SI1    2      0    
 3   P1    1     LYS     SI2    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
1   P5     1     ARG     BAS    1      0    
2   N0     1     ARG     SI1    2      0    
3   Qd     1     ARG     SI2    3    1.0    

[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      


;; ARGININE - NEUTRAL FORM

[ moleculetype ]
; molname       nrexcl
ARG0               1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     ARG0    BAS    1      0    
2   N0     1     ARG0    SI1    2      0    
3   P4     1     ARG0    SI2    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     BAS    1      0    
2   SC4    1     HIS     SI1    2    0    ; three side chains in triangle
3   SP1    1     HIS     SI2    3    0    ; configuration, mimicking
4   SP1    1     HIS     SI3    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
1   P5     1     HIS     BAS    1    0    
2   SC4    1     HIS     SI1    2    0    ; three side chains in triangle
3   SP1    1     HIS     SI2    3    0    ; configuration, mimicking
4   SQd    1     HIS     SI3    4   1.0   ; 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


;;; PHENYLALANINE

[ moleculetype ]
; molname       nrexcl
PHE                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     PHE     BAS    1    0
2   SC5    1     PHE     SI1    2    0    ; three side chains in triangle
3   SC5    1     PHE     SI2    3    0    ; configuration, mimicking
4   SC5    1     PHE     SI3    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


;;; TYROSINE

[ moleculetype ]
; molname       nrexcl
TYR                1

[ atoms ]
;id type resnr residu atom cgnr   charge
1   P5     1     TYR     BAS    1    0
2   SC4    1     TYR     SI1    2    0  
3   SC4    1     TYR     SI2    3    0 
4   SP1    1     TYR     SI3    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     BAS    1    0
2   SC4      1     TRP     SI1    2    0    
3   SNd      1     TRP     SI2    3    0
4   SC5      1     TRP     SI3    4    0
5   SC5      1     TRP     SI4    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