;Created by Kri on 06.03.2013
[ molecule ]
POPC

[ martini ]
NC3 PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B D3B C4B C5B

;
;NC3-PO4-GL1-C1B-C2B-D3B-C4B-C5B
;        |
;        GL2-C1A-C2A-C3A-C4A


[ mapping ]
gromos

[ atoms ]
; Terminal head group (choline)
    1   CN1   NC3 
    2   CN2
    3   CN3   
    4   NTM   
    5    CA   NC3 NC3 PO4
    6    CB   NC3 PO4 
; Phosphate group 
    7    OA   PO4 PO4 NC3
    8     P   PO4
    9    OB   
   10    OC   
   11    OD   PO4 PO4 GL1
; Diacylglycerol
   12    CC   GL1 GL1 PO4
   13    CD   GL1 
   14    OE   GL1 GL1 GL1 C1B
   15   C1A   GL1 C1B
   16    OF   
   17   C1B   C1B C1B C1B GL1
   18   C1C   C1B 
   19   C1D   C1B C1B C2B
   20   C1E   C1B C2B 
   21   C1F   C2B C2B C1B
   22   C1G   C2B 
   23   C1H   C2B D3B
   24   C1I   D3B D3B C2B
   25   C1J   D3B D3B C4B
   26   C1K   D3B C4B
   27   C1L   C4B
   28   C1M   C4B C4B C4B C5B
   29   C1N   C4B C4B C5B
   30   C1O   C5B C4B
   31   C1P   C5B C5B C4B
   32   C1Q   C5B C5B C5B C4B
   33   C1R   C5B
   34    CE   GL2
   35    OG   GL2 GL2 GL2 C1A
   36   C2A   GL2 C1A
   37    OH   
   38   C2B   C1A C1A C1A GL2
   39   C2C   C1A 
   40   C2D   C1A C1A C1A C2A
   41   C2E   C1A C2A
   42   C2F   C2A C2A C2A C1A
   43   C2G   C2A 
   44   C2H   C2A C2A C2A C3A
   45   C2I   C2A C3A 
   46   C2J   C3A C3A C3A C2A
   47   C2K   C3A
   48   C2L   C3A C3A C3A C4A
   49   C2M   C3A C4A
   50   C2N   C4A C4A C3A 
   51   C2O   C4A C4A C4A C3A
   52   C2P   C4A

;;;making a choline group
[out]
;CN2 NTM CN1 CA
[chiral]
;CN3 NTM CN1 CN2 CA

[ cis ]
;cis double bond
C1H C1I C1J C1K

; Acyl esters
; ===========
; This reconstruction is somewhat complex. Unfortunately
; the Gromos united atom force field does not have
; correct dihedrals for acyl esters and these groups
; have to be built with correct geometry. Only setting
; the C-O-CO-C dihedrals correct is not sufficient, as
; the distortions may be so large that the dihedrals
; are pushed over the barrier. Therefore, the whole
; glycerol group is rebuilt so as to form a buffer.

; Acyl ester 1
; ------------

[ chiral ]
x CD OE CE CC

[ trans ]
OF C1A CD x

[ out ]
OE C1A OF C1B

[ trans ]
C1B C1A OE CD

[ out ]
OF C1A OE C1B

; Acyl ester 2
; ------------

[ out ]
y CE CD OG

[ chiral ]
z CE OG CD y

[ trans ]
OH C2A CE z

[ out ]
OG C2A OH C2B

[ trans ]
C2B C2A OG CE

[ out ]
OH C2A OG C2B