; PHOSPHATIDILINOSITOL 3-MONO-PHOSPHATE - PIP1 with the phosphate at position 3
; with a PO tail (First a Palmitic acid or Stearoyl tail then a Palmitoleic acid or Oleic acid tail) therfore called POI1 (tail string would be -altail "CCDC CCCC")
; 
; Head based on Cesar Lopez DIPALMITOYLPHOSPHATIDILINOSITOL 3-MONO-PHOSPHATE ( PIP(3) ) named "PI3" from martini_v2.0_glycolipids.itp
; 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
  POI1         1

[ atoms ]
; id    type    resnr   residu  atom    cgnr    charge
   1        P1     1   POI1      C1      1          0       72.000
   2        P1     1   POI1      C2      2          0       72.000
   3        P4     1   POI1      C3      3          0       72.000
   4        Qa     1   POI1      CP      4         -1       72.000
   5        Qa     1   POI1      P1      5         -2       72.000
; Tail part (uses standar Martini v2.0 tail rules)
   6        Na     1   POI1      GL1     7          0       72.000
   7        Na     1   POI1      GL2     8          0       72.000
   8        C1     1   POI1      C1A     9          0       72.000
   9        C1     1   POI1      C2A    10          0       72.000
  10        C3     1   POI1      D3A    11          0       72.000
  11        C1     1   POI1      C4A    12          0       72.000
  12        C1     1   POI1      C1B    13          0       72.000
  13        C1     1   POI1      C2B    14          0       72.000
  14        C1     1   POI1      C3B    15          0       72.000
  15        C1     1   POI1      C4B    16          0       72.000

[ bonds ]
; i j   funct   length  force.c.
#ifdef FLEXIBLE
; Using bonds not constraints
  1     2         1 0.4 30000
  1     3         1 0.4 30000
  2     3         1 0.4 30000
  1     5         1 0.4 25000
  2     5         1 0.3 30000 
#endif
  1     4         1 0.35 1250
  4     6         1 0.47 1250
; Tail part (uses standar Martini v2.0 tail rules)
  6     7         1 0.37 1250
  6     8         1 0.47 1250
  8     9         1 0.47 1250
  9    10         1 0.47 1250
 10    11         1 0.47 1250
  7    12         1 0.47 1250
 12    13         1 0.47 1250
 13    14         1 0.47 1250
 14    15         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    6         2 140.00 25 ; link to lipid - PI has 30
; 4    6    7         2 120.00 25.0 ; These are part of the default lipids rules but not used here
; 4    6    8         2 180.00 25.0 ; These are part of the default lipids rules but not used here
; Tail part (uses standar Martini v2.0 tail rules)
  6     8     9         2 180.00 25.0
  8     9    10         2 180.00 25.0
  9    10    11         2 120.00 45.0
  7    12    13         2 180.00 25.0
 12    13    14         2 180.00 25.0
 13    14    15         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
  1     5         1 0.4
#endif

; Include Position restraint file
#ifdef POSRES
#include "POI1_posre.itp"
#endif
 
