;;;;;; Martini lipid topology for C(d18:1/24:1) GM3 (PNG3)
;
; Description:
;   A general model monosialodihexosylganglioside (GM3) lipid corresponding to atomistic e.g. C(d18:1/24:1) tails.
; Parameterization:
;   Head based on Cesar Lopez's GM1 see Lopez et al. 2013 with bonded parameters modified by Manuel Melo for
;   increased stability and faithfulness to AA. Top two galactose groups where cut off and the branching bead in 
;   GM1 (Nda) was changed to an SP1 type. The lipid tail follows the standard Martini 2.0 lipid definitions
;   and building block rules. The PN tail (first a Palmitic acid or Stearoyl tail then a Nervonic acid tail) has a 
;   tail string -altail "TCC CCCDCC".
; 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
;   H.I. Ingolfsson, M.N. Melo, F.J. van Eerden, C. Arnarez, C.A. Lopez, T.A. Wassenaar, X. Periole, A.H. De Vries, D.P. Tieleman,
;   S.J. Marrink. Lipid organization of the plasma membrane. JACS, 136:14554-14559, 2014. doi:10.1021/ja507832e
;   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
; Warning(s)/Note(s):
;   Note, GM3 currently runs at a 20fs time step. It also seems to be stable at 40fs, with no ill effect on the 
;   bonded distributions, although GROMACS will complain that bonds with k over 10000 have oscillation periods under 
;   10x the 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.
;   Note, seven of the bonds (flagged below) represent an average of an underlying multimodal distribution of the 
;   mapped AA, trajectory. These bonds should not be constrained since the average distance might correspond to a 
;   weakly populated position.
;

[ moleculetype ]
; molname      nrexcl
  PNG3         1

[ atoms ]
; id 	type 	resnr 	residu 	atom 	cgnr 	charge   mass
 1      SP1     1       PNG3     GM1     1      0        72.0000
 2      SP1     1       PNG3     GM2     2      0        72.0000
 3      SP1     1       PNG3     GM3     3      0        72.0000
 4      SP1     1       PNG3     GM4     4      0        72.0000
 5      SP1     1       PNG3     GM5     5      0        72.0000
 6      SP1     1       PNG3     GM6     6      0        72.0000 ; Changed from Nda to P1 - as it's not a branching bead any more
 7       Qa     1       PNG3     GM13   13     -1        72.0000
 8       P1     1       PNG3     GM14   14      0        72.0000
 9       P1     1       PNG3     GM15   15      0        72.0000
10       P5     1       PNG3     GM16   16      0        72.0000 ; 2016.05.10-changed from P4 to P5-Bead type and label in Fig.5 Lopez et al. 2013 were switched for GM16 and GM17
11       P4     1       PNG3     GM17   17      0        72.0000 ; 2016.05.10-changed from P5 to P4-Bead type and label in Fig.5 Lopez et al. 2013 were switched for GM16 and GM17
; Tail part
12       P1     1       PNG3     AM1    18      0        72.0000
13       P5     1       PNG3     AM2    19      0        72.0000
14       C3     1       PNG3     T1A    20      0        72.0000
15       C1     1       PNG3     C2A    21      0        72.0000
16       C1     1       PNG3     C3A    22      0        72.0000
17       C1     1       PNG3     C1B    25      0        72.0000
18       C1     1       PNG3     C2B    26      0        72.0000
19       C1     1       PNG3     C3B    27      0        72.0000
20       C3     1       PNG3     D4B    26      0        72.0000
21       C1     1       PNG3     C5B    29      0        72.0000
22       C1     1       PNG3     C6B    30      0        72.0000

[ bonds ]
; i j 	funct 	length 	force.c.
#ifdef FLEXIBLE
  4   5   1  0.389  40000
  4   6   1  0.300  40000
  7   8   1  0.35   35000
  7   9   1  0.381  35000
  8   9   1  0.364  40000
#endif
  1   2   1  0.36   17500 ; do not constrain (underlying mapped distribution is bimodal) 
  1   3   1  0.31   20000 ; do not constrain (underlying mapped distribution is bimodal)
  2   3   1  0.315   8500 ; do not constrain (underlying mapped distribution is multimodal)
  3   4   1  0.368  15000 ; do not constrain (underlying mapped distribution is bimodal)  
  5   6   1  0.307  25000 ; do not constrain (underlying mapped distribution is bimodal)
  6   7   1  0.376  12500
  8  10   1  0.34   11500 ; do not constrain (underlying mapped distribution is bimodal) 
  9  11   1  0.275   8500 
; Tail part 
  1 12   1  0.57   20000 ; Head linked to AM1
 12 13   1  0.27   20000 ; Based on Cesar GM1 and GCER
 12 14   1  0.29   20000 ; Based on Cesar GM1 and GCER
 14 15   1  0.47   1250 
 15 16   1  0.47   1250
 13 17   1  0.37   20000 ; Based on Cesar GM1 and GCER
 17 18   1  0.47   1250
 18 19   1  0.47   1250
 19 20   1  0.47   1250
 20 21   1  0.47   1250
 21 22   1  0.47   1250

[ angles ]
; i j k 	funct 	angle 	force.c.
  2   3   4   2    85.50  320.00
  3   4   5   2    67.00  550.00
  4   6   7   2    97.50  295.00
  6   7   9   2    71.00  700.00
  7   9  11   2    96.00  210.00
  9   8  10   2    61.00  300.00
; Orient Head
  3   1  12   2    50.00  200.00  
; Tail part
  1  12  13   2    85.00   25.00  ; Based on Cesar GM1 and GCER
  1  12  14   2   150.00   30.00  ; Based on Cesar GM1 and GCER
 12  13  17   2   129.00  200.00  ; Based on Cesar GM1 and GCER
 12  14  15   2   180.00   25.00  ; Based on Cesar GM1 and GCER
 14  15  16   2   180.00   25.00
 13  17  18   2   180.00   25.00
 17  18  19   2   180.00   25.00 
 18  19  20   2   180.00   25.00
 19  20  21   2   120.00   45.00
 20  21  22   2   180.00   25.00

[ dihedrals ]
  1   2   3   4   2  -160.0  30.0
  2   3   4   5   2  -149.0  16.0
  3   4   5   6   2  -150.0  55.0
  4   6   7   9   2  -124.0  60.0
  5   4   6   7   2   154.0 115.0
  6   7   9   8   2   107.5 265.0
  7   9   8  10   2   137.0  80.0
  8   7   9  11   2   162.0  50.0
  3   1  12  13   1   125.0  10.0  1 ; Orient head with respect to tail 

#ifndef FLEXIBLE
[ constraints ]
  4   5   1  0.389  40000
  4   6   1  0.300  40000
  7   8   1  0.35   35000
  7   9   1  0.381  35000
  8   9   1  0.364  40000
#endif

[ exclusions ]
  2  4
  3  5
  6  9
  9 10


; Include Position restraint file
#ifdef POSRES
#include "PNG3_posre.itp"
#endif
