; PHOSPHATIDILINOSITOL 3-4-5 tri-PHOSPHATE - PIP3 with the phosphates at position 3, 4 and 5
; with a PO tail (First a Palmitic acid or Stearoyl tail then a Palmitoleic acid or Oleic acid tail) therfore called POI7 (tail string would be -altail "CCDC CCCC")
;
; WARNING this one is losly based on Cesar Lopez DIPALMITOYLPHOSPHATIDILINOSITOL 3-4 BI-PHOSPHATE ( PIP2(3,4) ) named "PI34" from martini_v2.0_glycolipids.itp
; Was just placed opposite to the P1 – this needs to be redone with proper mapping from atomistic simulations as the C1, C2, C3 beads are not evenly distributed 
; on the inositol ring. Also charge state should be altered / check – at pH 7, PIP3 normally has one or two reduced charges. 
; - Also dihedral for head oriantation was removed to make the molecule more stable - should be tested / compaired to atomistic sims
; 
; Note: bonds with force constant > 25000 are treated as constraints, but use harmonic bonds for minimization. 
;       Add define=-DFLEXIBLE to select harmonic bonds for minimization purposes.
;


[ moleculetype ]
; molname      nrexcl
POI7               1

[ atoms ]
; id    type    resnr   residu  atom    cgnr    charge
   1        P1     1   POI7      C1      1          0       72.000
   2        Na     1   POI7      C2      2          0       72.000
   3        P4     1   POI7      C3      3          0       72.000
   4        Qa     1   POI7      CP      4         -1       72.000
   5        Qa     1   POI7      P1      5         -2       72.000
   6        Qa     1   POI7      P2      6         -2       72.000
   7        Qa     1   POI7      P3      7         -2       72.000 ; New P3 bead
; Tail part (uses standar Martini v2.0 tail rules)
   8        Na     1   POI7      GL1     8          0       72.000
   9        Na     1   POI7      GL2     9          0       72.000
  10        C1     1   POI7      C1A    10          0       72.000
  11        C1     1   POI7      C2A    11          0       72.000
  12        C3     1   POI7      D3A    12          0       72.000
  13        C1     1   POI7      C4A    13          0       72.000
  14        C1     1   POI7      C1B    14          0       72.000
  15        C1     1   POI7      C2B    15          0       72.000
  16        C1     1   POI7      C3B    16          0       72.000
  17        C1     1   POI7      C4B    17          0       72.000

[ bonds ]
; i j   funct   length  force.c.i
#ifdef FLEXIBLE
; Using bonds not constraints
  1     2         1 0.4 30000
  1     3         1 0.4 30000
  2     3         1 0.4 30000
  2     5         1 0.3  30000
  2     6         1 0.35 30000
  1     5         1 0.40 25000
  3     6         1 0.31 30000
;  5     6         1 0.60 25000
  1     7         1 0.40 25000 ; New to add P3 bad - not messured just placed 
  3     7         1 0.3  30000 ; New to add P3 bad - not messured just placed
;  6     7         1 0.60 25000 ; New to add P3 bad - not messured just placed
#endif
  5     6         1 0.60 25000 ; added just as bonds to increase stability
  6     7         1 0.60 25000 ; New to add P3 bad - not messured just placed ; added just as bonds to increase stability
  1     4         1 0.35 1250
  4     8         1 0.47 1250
; Tail part (uses standar Martini v2.0 tail rules)
  8     9         1 0.37 1250
  8    10         1 0.47 1250
 10    11         1 0.47 1250
 11    12         1 0.47 1250
 12    13         1 0.47 1250
  9    14         1 0.47 1250
 14    15         1 0.47 1250
 15    16         1 0.47 1250
 16    17         1 0.47 1250

[ angles ]
; i j k         funct   angle   force.c.
; Here we have less angles than in PI, replaced by bonds/constraints
; Orient Head
  1    4    8         2 140.00 25 ; link to lipid - PI has 30
; 4    8    9         2 120.00 25.0 ; These are part of the default lipids rules but not used here
; 4    8   10         2 180.00 25.0 ; These are part of the default lipids rules but not used here
  8    10    11         2 180.00 25.0
 10    11    12         2 180.00 25.0
 11    12    13         2 120.00 45.0
  9    14    15         2 180.00 25.0 
 14    15    16         2 180.00 25.0 
 15    16    17         2 180.00 25.0 

[ dihedrals ]
;3 1 4 5 1 -30.00 5.00 1   ; Removed as it was unstable - WARNING has not been tested

[ constraints ]
#ifndef FLEXIBLE 
; Using constraints not bonds
  1     2         1 0.4 
  1     3         1 0.4 
  2     3         1 0.4 
  2     5         1 0.3  
  2     6         1 0.35 
  1     5         1 0.40 
  3     6         1 0.31 
;  5     6         1 0.60 ; added just as bonds to increase stability
  1     7         1 0.40 ; New to add P3 bad - not messured just placed
  3     7         1 0.3  ; New to add P3 bad - not messured just placed
;  6     7         1 0.60 ; New to add P3 bad - not messured just placed ; added just as bonds to increase stability
#endif

; Include Position restraint file
#ifdef POSRES
#include "POI7_posre.itp"
#endif
 
