;;;;;; Martini lipid topology for C(d18:1/24:1) GS (PNGS)
;
; Description:
;   A general model glucosylceramide or galactosylceramide (GS) lipid corresponding to atomistic e.g. C(d18:1/24:1) tails
; Parameterization:
;   See Lopez et al. 2013 
; Reference(s):
;   C.A. Lopez, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids. JCTC,
;   9:1694-1708, 2013. doi:10.1021/ct3009655
;   S.J. Marrink, A.H. de Vries, A.E. Mark. Coarse grained model for semi-quantitative lipid simulations. JPC-B, 108:750-760,
;   2004. doi:10.1021/jp036508g
;   S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. The MARTINI force field: coarse grained model for
;   biomolecular simulations. JPC-B, 111:7812-7824, 2007. doi:10.1021/jp071097f
; Created: 2015.04.20
; Author(s): Cesar Lopez <c.a.lopez-bautista@rug.nl> and Siewert Marrink <s.j.marrink@rug.nl>
; Warning(s)/Note(s):
;   Note, is stable with a 20 fs time step.
;   Note, most 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 ]
PNGS               1

[ atoms ]
    1          P4    1    PNGS     C1     1         0        72.0000
    2          P1    1    PNGS     C2     2         0        72.0000
    3          P1    1    PNGS     C3     3         0        72.0000
    4          P1    1    PNGS    AM1     4         0        72.0000
    5          P5    1    PNGS    AM2     5         0        72.0000
    6          C3    1    PNGS    T1A     6         0        72.0000 ; corrected (C3 instead of C1), oct 2013
    7          C1    1    PNGS    C2A     7         0        72.0000
    8          C1    1    PNGS    C3A     8         0        72.0000
    9          C1    1    PNGS    C4A     9         0        72.0000
   10          C1    1    PNGS    C1B    10         0        72.0000
   11          C1    1    PNGS    C2B    11         0        72.0000
   12          C1    1    PNGS    C3B    12         0        72.0000
   13          C3    1    PNGS    D4B    13         0        72.0000
   14          C1    1    PNGS    C5B    14         0        72.0000
   15          C1    1    PNGS    C6B    15         0        72.0000
   
[ bonds ]
    3    4   1  0.57   20000
    4    5   1  0.27   20000 ; AM1-AM2
    4    6   1  0.29   20000 ; AM1-D1A ; corrected (0.29 instead of 0.37), oct 2013
    6    7   1  0.470  1250
    7    8   1  0.470  1250
    8    9   1  0.470  1250
    5   10   1  0.37   20000 ; AM2-C1B ; corrected (0.37 instead of 0.29), oct 2013
   10   11   1  0.470  1250
   11   12   1  0.470  1250
   12   13   1  0.470  1250
   13   14   1  0.470  1250
   14   15   1  0.470  1250
#ifdef FLEXIBLE
    1    2   1  0.3    30000
    1    3   1  0.3    30000
    2    3   1  0.3    30000
#else
[ constraints ]
    1    2   1  0.3    
    1    3   1  0.3    
    2    3   1  0.3  
#endif

[ angles ]
   1     3     4    2    50.00  200.00 ; ring flipping
   3     4     5    2    85.00   25.00 ; link to lipid
   3     4     6    2   150.00   30.00 ; link to lipid
  10     5     4    2   129.00  200.00 ; linkage
   4     6     7    2   180.00   45.00 ; HII change to 45 to fit the trans double bond building block
   6     7     8    2   180.00   25.00
   7     8     9    2   180.00   25.00
   5    10    11    2   180.00   25.00
  10    11    12    2   180.00   25.00
  11    12    13    2   180.00   25.00
  12    13    14    2   120.00   45.00
  13    14    15    2   180.00   25.00

[ dihedrals ]
 1 3 4 5 1   125.0    10.00 1 ; ring orientation 
  


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

