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martini_v2.0_lipids.itp
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;;;;;; TOPOLOGIES FOR LIPIDS - last updated 15-march-2011
;
; lipids are defined here as double tail amphipatic molecules
; (for mono-tailed lipids see the surfactant files)
; (for pegylated lipids see the polymer files)
;
; currently available:
;;;;;; COMMON PCs: DPPC, DHPC, DLPC (DMPC), DSPC, POPC, DOPC, DAPC, DUPC
;;;;;; COMMON PEs: DPPE, DHPE, DLPE (DMPE), DSPE, POPE, DOPE
;;;;;; SPHINGOLIPIDS: PPCS
;;;;;; CHARGED LIPIDS: DOPG, POPG, DOPS, POPS
; For more background on the testing and optimization of the parameters,
; please see the following refs:
; S.J. Marrink, A.H. de Vries, A.E. Mark.
; Coarse grained model for semi-quantitative lipid simulations.
; JPC-B, 108:750-760, 2004.
; and for poly-unsaturated lipids:
; S.J. Marrink, A.H. de Vries, T.A. Harroun, J. Katsaras, S.R. Wassall.
; Cholesterol shows preference for the interior of polyunsaturated lipid membranes.
; JACS, 130:10-11, 2008.
;
; and
;
; H.J. Risselada, S.J. Marrink.
; The molecular face of lipid rafts in model membranes.
; PNAS, 105:17367-17372, 2008.
;;;;;;
;;;;;; COMMON PCs
;;;;;;
;;;;;; DIPALMITOYL PHOSPHATIDYLCHOLINE
;
; in general models PCs with saturated tail lengths C15-18
[moleculetype]
; molname nrexcl
DPPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DPPC NC3 1 1.0
2 Qa 1 DPPC PO4 2 -1.0
3 Na 1 DPPC GL1 3 0
4 Na 1 DPPC GL2 4 0
5 C1 1 DPPC C1A 5 0
6 C1 1 DPPC C2A 6 0
7 C1 1 DPPC C3A 7 0
8 C1 1 DPPC C4A 8 0
9 C1 1 DPPC C1B 9 0
10 C1 1 DPPC C2B 10 0
11 C1 1 DPPC C3B 11 0
12 C1 1 DPPC C4B 12 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
4 9 1 0.470 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
4 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
;;;;;; DIHEXANOYL PHOSPHATIDYLCHOLINE
;
; in general models PCs with saturated tail lengths C8-11
[moleculetype]
; molname nrexcl
DHPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DHPC NC3 1 1.0
2 Qa 1 DHPC PO4 2 -1.0
3 Na 1 DHPC GL1 3 0
4 Na 1 DHPC GL2 4 0
5 C1 1 DHPC C1A 5 0
6 C1 1 DHPC C2A 6 0
7 C1 1 DHPC C1B 7 0
8 C1 1 DHPC C2B 8 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
4 7 1 0.470 1250
7 8 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
4 7 8 2 180.0 25.0
;;;;;; DILAUROYL PHOSPHATIDYLCHOLINE
;
; in general models PCs with saturated tail lengths C12-15, including DMPC
[moleculetype]
; molname nrexcl
DLPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DLPC NC3 1 1.0
2 Qa 1 DLPC PO4 2 -1.0
3 Na 1 DLPC GL1 3 0
4 Na 1 DLPC GL2 4 0
5 C1 1 DLPC C1A 5 0
6 C1 1 DLPC C2A 6 0
7 C1 1 DLPC C3A 7 0
8 C1 1 DLPC C1B 8 0
9 C1 1 DLPC C2B 9 0
10 C1 1 DLPC C3B 10 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
4 8 1 0.47 1250
8 9 1 0.47 1250
9 10 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
4 8 9 2 180.0 25.0
8 9 10 2 180.0 25.0
;;;;;; DISTEAROYL PHOSPHATIDYLCHOLINE
;
; in general models PCs with saturated tail lengths C18-21
[moleculetype]
; molname nrexcl
DSPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DSPC NC3 1 1.0
2 Qa 1 DSPC PO4 2 -1.0
3 Na 1 DSPC GL1 3 0
4 Na 1 DSPC GL2 4 0
5 C1 1 DSPC C1A 5 0
6 C1 1 DSPC C2A 6 0
7 C1 1 DSPC C3A 7 0
8 C1 1 DSPC C4A 8 0
9 C1 1 DSPC C5A 9 0
10 C1 1 DSPC C1B 10 0
11 C1 1 DSPC C2B 11 0
12 C1 1 DSPC C3B 12 0
13 C1 1 DSPC C4B 13 0
14 C1 1 DSPC C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
7 8 9 2 180.0 25.0
4 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
11 12 13 2 180.0 25.0
12 13 14 2 180.0 25.0
;;;;;; PALMITOYL OLEOYL PHOSPHATIDYLCOLINE
[moleculetype]
; molname nrexcl
POPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 POPC NC3 1 1.0
2 Qa 1 POPC PO4 2 -1.0
3 Na 1 POPC GL1 3 0
4 Na 1 POPC GL2 4 0
5 C1 1 POPC C1A 5 0
6 C1 1 POPC C2A 6 0
7 C1 1 POPC C3A 7 0
8 C1 1 POPC C4A 8 0
9 C1 1 POPC C1B 9 0
10 C1 1 POPC C2B 10 0
11 C3 1 POPC D3B 11 0
12 C1 1 POPC C4B 12 0
13 C1 1 POPC C5B 13 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
4 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
3 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 9 2 180.0 25.0
4 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
3 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 120.0 45.0
11 12 13 2 180.0 25.0
;;;;;; DIOLEOYL PHOSPHATIDYLCHOLINE
[moleculetype]
; molname nrexcl
DOPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DOPC NC3 1 1.0
2 Qa 1 DOPC PO4 2 -1.0
3 Na 1 DOPC GL1 3 0
4 Na 1 DOPC GL2 4 0
5 C1 1 DOPC C1A 5 0
6 C1 1 DOPC C2A 6 0
7 C3 1 DOPC D3A 7 0
8 C1 1 DOPC C4A 8 0
9 C1 1 DOPC C5A 9 0
10 C1 1 DOPC C1B 10 0
11 C1 1 DOPC C2B 11 0
12 C3 1 DOPC D3B 12 0
13 C1 1 DOPC C4B 13 0
14 C1 1 DOPC C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 120.0 45.0
7 8 9 2 180.0 25.0
4 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
11 12 13 2 120.0 45.0
12 13 14 2 180.0 25.0
;;;;;; DIARACHIDONOYL PHOSPHATIDYLCHOLINE (20:4-20:4 PC)
;;;;;; or di-(all-cis-5,8,11,14-eicosatetraenoyl)-PC
[ moleculetype ]
; molname nrexcl
DAPC 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 Q0 1 DAPC NC3 1 1.0
2 Qa 1 DAPC PO4 2 -1.0
3 Na 1 DAPC GL1 3 0
4 Na 1 DAPC GL2 4 0
5 C4 1 DAPC D1A 5 0
6 C4 1 DAPC D2A 6 0
7 C4 1 DAPC D3A 7 0
8 C4 1 DAPC D4A 8 0
9 C2 1 DAPC C5A 9 0
10 C4 1 DAPC D1B 10 0
11 C4 1 DAPC D2B 11 0
12 C4 1 DAPC D3B 12 0
13 C4 1 DAPC D4B 13 0
14 C2 1 DAPC C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.000 25.0
2 3 5 2 180.000 25.0
3 5 6 2 100.000 10.0
5 6 7 2 100.000 10.0
6 7 8 2 100.000 10.0
7 8 9 2 120.000 45.0
4 10 11 2 100.000 10.0
10 11 12 2 100.000 10.0
11 12 13 2 100.000 10.0
12 13 14 2 120.000 45.0
;;;;;; DILINOLEYL PHOSPHATIDYLCHOLINE (18:2-18:2 PC)
;;;;;; or di-(cis-cis-9,12-octadecadienoyl)-PC
;
[moleculetype]
; molname nrexcl
DUPC 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 DUPC NC3 1 1.0
2 Qa 1 DUPC PO4 2 -1.0
3 Na 1 DUPC GL1 3 0
4 Na 1 DUPC GL2 4 0
5 C1 1 DUPC C1A 5 0
6 C4 1 DUPC D2A 6 0
7 C4 1 DUPC D3A 7 0
8 C1 1 DUPC C4A 8 0
9 C1 1 DUPC C1B 9 0
10 C4 1 DUPC D2B 10 0
11 C4 1 DUPC D3B 11 0
12 C1 1 DUPC C4B 12 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
4 9 1 0.470 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 100.0 10.0
6 7 8 2 120.0 45.0
4 9 10 2 180.0 25.0
9 10 11 2 100.0 10.0
10 11 12 2 120.0 45.0
;;;;;;
;;;;;; COMMON PEs
;;;;;;
;;;;;; DPPE, DHPE, DLPE, DSPE, POPE, DOPE
;;;;;;
;;;;;; DIPALMITOYL PHOSPHATIDYLETHANOLAMINE
;
; in general models PEs with saturated tail lengths C15-18
[moleculetype]
; molname nrexcl
DPPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 Qd 1 DPPE NH3 1 1.0
2 Qa 1 DPPE PO4 2 -1.0
3 Na 1 DPPE GL1 3 0
4 Na 1 DPPE GL2 4 0
5 C1 1 DPPE C1A 5 0
6 C1 1 DPPE C2A 6 0
7 C1 1 DPPE C3A 7 0
8 C1 1 DPPE C4A 8 0
9 C1 1 DPPE C1B 9 0
10 C1 1 DPPE C2B 10 0
11 C1 1 DPPE C3B 11 0
12 C1 1 DPPE C4B 12 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
4 9 1 0.470 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
4 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
;;;;;; DIHEXANOYL PHOSPHATIDYLETHANOLAMINE
;
; in general models PEs with saturated tail lengths C8-11
[moleculetype]
; molname nrexcl
DHPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 Qd 1 DHPE NH3 1 1.0
2 Qa 1 DHPE PO4 2 -1.0
3 Na 1 DHPE GL1 3 0
4 Na 1 DHPE GL2 4 0
5 C1 1 DHPE C1A 5 0
6 C1 1 DHPE C2A 6 0
7 C1 1 DHPE C1B 7 0
8 C1 1 DHPE C2B 8 0
[bonds]
; i j funct length force.c.
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.370 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
4 7 1 0.470 1250
7 8 1 0.470 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
4 7 8 2 180.0 25.0
;;;;;; DILAUROYL PHOSPHATIDYLETHANOLAMINE
;
; in general models PEs with saturated tail lengths C12-15, including DMPE
[moleculetype]
; molname nrexcl
DLPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 Qd 1 DLPE NH3 1 1.0
2 Qa 1 DLPE PO4 2 -1.0
3 Na 1 DLPE GL1 3 0
4 Na 1 DLPE GL2 4 0
5 C1 1 DLPE C1A 5 0
6 C1 1 DLPE C2A 6 0
7 C1 1 DLPE C3A 7 0
8 C1 1 DLPE C1B 8 0
9 C1 1 DLPE C2B 9 0
10 C1 1 DLPE C3B 10 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
4 8 1 0.47 1250
8 9 1 0.47 1250
9 10 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
4 8 9 2 180.0 25.0
8 9 10 2 180.0 25.0
;;;;;; DISTEAROYL PHOSPHATIDYLETHANOLAMINE
;
; in general models PEs with saturated tail lengths C18-21
[moleculetype]
; molname nrexcl
DSPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 Qd 1 DSPE NH3 1 1.0
2 Qa 1 DSPE PO4 2 -1.0
3 Na 1 DSPE GL1 3 0
4 Na 1 DSPE GL2 4 0
5 C1 1 DSPE C1A 5 0
6 C1 1 DSPE C2A 6 0
7 C1 1 DSPE C3A 7 0
8 C1 1 DSPE C4A 8 0
9 C1 1 DSPE C5A 9 0
10 C1 1 DSPE C1B 10 0
11 C1 1 DSPE C2B 11 0
12 C1 1 DSPE C3B 12 0
13 C1 1 DSPE C4B 13 0
14 C1 1 DSPE C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
7 8 9 2 180.0 25.0
4 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
11 12 13 2 180.0 25.0
12 13 14 2 180.0 25.0
;;;;;; PALMITOYL OLEOYL PHOSPHATIDYLETHANOLAMINE
[moleculetype]
; molname nrexcl
POPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 Qd 1 POPE NH3 1 1.0
2 Qa 1 POPE PO4 2 -1.0
3 Na 1 POPE GL1 3 0
4 Na 1 POPE GL2 4 0
5 C1 1 POPE C1A 5 0
6 C1 1 POPE C2A 6 0
7 C1 1 POPE C3A 7 0
8 C1 1 POPE C4A 8 0
9 C1 1 POPE C1B 9 0
10 C1 1 POPE C2B 10 0
11 C3 1 POPE D3B 11 0
12 C1 1 POPE C4B 12 0
13 C1 1 POPE C5B 13 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
4 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
3 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 9 2 180.0 25.0
4 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
3 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 120.0 45.0
11 12 13 2 180.0 25.0
;;;;;; DIOLEOYL PHOSPHATIDYLETHANOLAMINE
[moleculetype]
; molname nrexcl
DOPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 Qd 1 DOPE NH3 1 1.0
2 Qa 1 DOPE PO4 2 -1.0
3 Na 1 DOPE GL1 3 0
4 Na 1 DOPE GL2 4 0
5 C1 1 DOPE C1A 5 0
6 C1 1 DOPE C2A 6 0
7 C3 1 DOPE D3A 7 0
8 C1 1 DOPE C4A 8 0
9 C1 1 DOPE C5A 9 0
10 C1 1 DOPE C1B 10 0
11 C1 1 DOPE C2B 11 0
12 C3 1 DOPE D3B 12 0
13 C1 1 DOPE C4B 13 0
14 C1 1 DOPE C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 120.0 45.0
7 8 9 2 180.0 25.0
4 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
11 12 13 2 120.0 45.0
12 13 14 2 180.0 25.0
;;;;;;
;;;;;; SPHINGHOLIPIDS
;;;;;;
;;;;;; PPCS, ...
;;;;;; PALMITOYL SPHINGOMYELINE PC
; not tested!!
[moleculetype]
; molname nrexcl
PPCS 1
[atoms]
; id type resnr residu atom cgnr charge
1 Q0 1 PPCS NC3 1 1.0
2 Qa 1 PPCS PO4 2 -1.0
3 P5 1 PPCS AM1 3 0
4 P1 1 PPCS AM2 4 0
5 C1 1 PPCS C1A 5 0
6 C1 1 PPCS C2A 6 0
7 C1 1 PPCS C3A 7 0
8 C1 1 PPCS C4A 8 0
9 C3 1 PPCS D1B 9 0
10 C1 1 PPCS C2B 10 0
11 C1 1 PPCS C3B 11 0
12 C1 1 PPCS C4B 12 0
[bonds]
; i j funct length force.c.
1 2 1 0.47 1250
2 3 1 0.47 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
4 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 5 2 180.0 25.0
3 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
4 9 10 2 180.0 45.0
9 10 11 2 180.0 25.0
10 11 12 2 180.0 25.0
;;;;;;
;;;;;; CHARGED LIPIDS
;;;;;;
;;;;;; DOPG, POPG, DOPS, POPS
;;;;;;
;;;;;; Contributed by Luca Monticelli
;;;;;;
;;;;;; Note: the topologies for charged lipids are not well tested (yet),
;;;;;; but have been used in, e.g., monolayer studies :
;;;;;; S. Baoukina, L. Monticelli, H.J. Risselada, S.J. Marrink, D.P. Tieleman.
;;;;;; The molecular mechanism of lipid monolayer collapse.
;;;;;; PNAS, 105:10803-10808, 2008.
;;;;;; DIOLEOYL PHOSPHATIDYLGLYCEROL
;
; trial topology!
[ moleculetype ]
; molname nrexcl
DOPG 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P4 1 DOPG GL0 1 0
2 Qa 1 DOPG PO4 2 -1.0
3 Na 1 DOPG GL1 3 0
4 Na 1 DOPG GL2 4 0
5 C1 1 DOPG C1A 5 0
6 C1 1 DOPG C2A 6 0
7 C3 1 DOPG D3A 7 0
8 C1 1 DOPG C4A 8 0
9 C1 1 DOPG C5A 9 0
10 C1 1 DOPG C1B 10 0
11 C1 1 DOPG C2B 11 0
12 C3 1 DOPG D3B 12 0
13 C1 1 DOPG C4B 13 0
14 C1 1 DOPG C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.37 1250
2 3 1 0.37 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.000 25.0
2 3 5 2 180.000 25.0
3 5 6 2 180.000 25.0
5 6 7 2 180.000 25.0
6 7 8 2 120.000 45.0
7 8 9 2 180.000 25.0
4 10 11 2 180.000 25.0
10 11 12 2 180.000 25.0
11 12 13 2 120.000 45.0
12 13 14 2 180.000 25.0
;;;;;; PALMITOYL OLEOYL PHOSPHATIDYLGLYCEROL
;
; trial topology!
; note: in earlier version of this file (before 15-3-2011), actually OPPG rather than POPG was modeled
; (in practice the behavior is expected to be very similar though)
[ moleculetype ]
; molname nrexcl
POPG 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P4 1 POPG GL0 1 0
2 Qa 1 POPG PO4 2 -1.0
3 Na 1 POPG GL1 3 0
4 Na 1 POPG GL2 4 0
5 C1 1 POPG C1A 5 0
6 C1 1 POPG C2A 6 0
7 C1 1 POPG C3A 7 0
8 C1 1 POPG C4A 8 0
9 C1 1 POPG C1B 9 0
10 C1 1 POPG C2B 10 0
11 C3 1 POPG D3B 11 0
12 C1 1 POPG C4B 12 0
13 C1 1 POPG C5B 13 0
[bonds]
; i j funct length force.c.
1 2 1 0.37 1250
2 3 1 0.37 1250
3 4 1 0.37 1250
4 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
3 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 9 2 180.0 25.0
4 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
3 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0
10 11 12 2 120.0 45.0
11 12 13 2 180.0 25.0
;;;;;; DI-OLEOYL PHOSPHATIDYLSERINE
;
; trial topology!
[ moleculetype ]
; molname nrexcl
DOPS 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P5 1 DOPS CNO 1 0
2 Qa 1 DOPS PO4 2 -1.0
3 Na 1 DOPS GL1 3 0
4 Na 1 DOPS GL2 4 0
5 C1 1 DOPS C1A 5 0
6 C1 1 DOPS C2A 6 0
7 C3 1 DOPS D3A 7 0
8 C1 1 DOPS C4A 8 0
9 C1 1 DOPS C5A 9 0
10 C1 1 DOPS C1B 10 0
11 C1 1 DOPS C2B 11 0
12 C3 1 DOPS D3B 12 0
13 C1 1 DOPS C4B 13 0
14 C1 1 DOPS C5B 14 0
[bonds]
; i j funct length force.c.
1 2 1 0.37 1250
2 3 1 0.37 1250
3 4 1 0.37 1250
3 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
8 9 1 0.47 1250
4 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
13 14 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.000 25.0
2 3 5 2 180.000 25.0
3 5 6 2 180.000 25.0
5 6 7 2 180.000 25.0
6 7 8 2 120.000 45.0
7 8 9 2 180.000 25.0
4 10 11 2 180.000 25.0
10 11 12 2 180.000 25.0
11 12 13 2 120.000 45.0
12 13 14 2 180.000 25.0
;;;;;; PALMITOYL OLEOYL PHOSPHATIDYLSERINE
;
; trial topology!
; note: in earlier version of this file (before 15-3-2011), actually OPPS rather than POPS was modeled
; (in practice the behavior is expected to be very similar though)
[ moleculetype ]
; molname nrexcl
POPS 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P5 1 POPS CNO 1 0
2 Qa 1 POPS PO4 2 -1.0
3 Na 1 POPS GL1 3 0
4 Na 1 POPS GL2 4 0
5 C1 1 POPS C1A 5 0
6 C1 1 POPS C2A 6 0
7 C1 1 POPS C3A 7 0
8 C1 1 POPS C4A 8 0
9 C1 1 POPS C1B 9 0
10 C1 1 POPS C2B 10 0
11 C3 1 POPS D3B 11 0
12 C1 1 POPS C4B 12 0
13 C1 1 POPS C5B 13 0
[bonds]
; i j funct length force.c.
1 2 1 0.37 1250
2 3 1 0.37 1250
3 4 1 0.37 1250
4 5 1 0.47 1250
5 6 1 0.47 1250
6 7 1 0.47 1250
7 8 1 0.47 1250
3 9 1 0.47 1250
9 10 1 0.47 1250
10 11 1 0.47 1250
11 12 1 0.47 1250
12 13 1 0.47 1250
[angles]
; i j k funct angle force.c.
2 3 4 2 120.0 25.0
2 3 9 2 180.0 25.0
4 5 6 2 180.0 25.0
5 6 7 2 180.0 25.0
6 7 8 2 180.0 25.0
3 9 10 2 180.0 25.0
9 10 11 2 180.0 25.0