Hi GMX Users,
I have generated a topology entry for the DOPC lipid for
charmm27.ff/lipids.rtp
by copying and editing the entry of POPC. My DOPC has passed two simple
tests
with gromacs-4.5.3 on a test structure of an isolated model molecule
(generated with CHARMM)
1) energy minimization produced a reasonable structure close to starting
coordinates
2) all energy components agreed with CHARMM v. 27 results to at least 4
digits.
I enclose my topology file; I would welcome
- information about other DOPC topologies in GMX
- critical comments
- suggestions for more simple tests ( the 100 ns solvated bilayer
simulation is already on my list)
Greetings
Krzysztof Kuczera
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
[ DOPC ]
[ atoms ]
N NTL -0.60 0
C11 CTL2 -0.10 1
C12 CTL5 -0.35 2
C13 CTL5 -0.35 3
C14 CTL5 -0.35 4
H11 HL 0.25 5
H12 HL 0.25 6
H21 HL 0.25 7
H22 HL 0.25 8
H23 HL 0.25 9
H31 HL 0.25 10
H32 HL 0.25 11
H33 HL 0.25 12
H41 HL 0.25 13
H42 HL 0.25 14
H43 HL 0.25 15
C15 CTL2 -0.08 16
H51 HAL2 0.09 17
H52 HAL2 0.09 18
P1 PL 1.50 19
O3 O2L -0.78 20
O4 O2L -0.78 21
O1 OSL -0.57 22
O2 OSL -0.57 23
C1 CTL2 -0.08 24
HA HAL2 0.09 25
HB HAL2 0.09 26
C2 CTL1 0.04 27
HS HAL1 0.09 28
O21 OSL -0.34 29
C21 CL 0.63 30
O22 OBL -0.52 31
C22 CTL2 -0.08 32
H2R HAL2 0.09 33
H2S HAL2 0.09 34
C3 CTL2 -0.05 35
HX HAL2 0.09 36
HY HAL2 0.09 37
O31 OSL -0.34 38
C31 CL 0.63 39
O32 OBL -0.52 40
C32 CTL2 -0.08 41
H2X HAL2 0.09 42
H2Y HAL2 0.09 43
C23 CTL2 -0.18 44
H3R HAL2 0.09 45
H3S HAL2 0.09 46
C24 CTL2 -0.18 47
H4R HAL2 0.09 48
H4S HAL2 0.09 49
C25 CTL2 -0.18 50
H5R HAL2 0.09 51
H5S HAL2 0.09 52
C26 CTL2 -0.18 53
H6R HAL2 0.09 54
H6S HAL2 0.09 55
C27 CTL2 -0.18 56
H7R HAL2 0.09 57
H7S HAL2 0.09 58
C28 CTL2 -0.18 59
H8R HAL2 0.09 60
H8S HAL2 0.09 61
C29 CEL1 -0.15 62
H91 HEL1 0.15 63
C210 CEL1 -0.15 64
H101 HEL1 0.15 65
C211 CTL2 -0.18 66
H11R HAL2 0.09 67
H11S HAL2 0.09 68
C212 CTL2 -0.18 69
H12R HAL2 0.09 70
H12S HAL2 0.09 71
C213 CTL2 -0.18 72
H13R HAL2 0.09 73
H13S HAL2 0.09 74
C214 CTL2 -0.18 75
H14R HAL2 0.09 76
H14S HAL2 0.09 77
C215 CTL2 -0.18 78
H15R HAL2 0.09 79
H15S HAL2 0.09 80
C216 CTL2 -0.18 81
H16R HAL2 0.09 82
H16S HAL2 0.09 83
C217 CTL2 -0.18 84
H17R HAL2 0.09 85
H17S HAL2 0.09 86
C218 CTL3 -0.27 87
H18R HAL3 0.09 88
H18S HAL3 0.09 89
H18T HAL3 0.09 90
C33 CTL2 -0.18 91
H3X HAL2 0.09 92
H3Y HAL2 0.09 93
C34 CTL2 -0.18 94
H4X HAL2 0.09 95
H4Y HAL2 0.09 96
C35 CTL2 -0.18 97
H5X HAL2 0.09 98
H5Y HAL2 0.09 99
C36 CTL2 -0.18 100
H6X HAL2 0.09 101
H6Y HAL2 0.09 102
C37 CTL2 -0.18 103
H7X HAL2 0.09 104
H7Y HAL2 0.09 105
C38 CTL2 -0.18 106
H8X HAL2 0.09 107
H8Y HAL2 0.09 108
C39 CEL1 -0.15 109
H92 HEL1 0.15 110
C310 CEL1 -0.15 111
H102 HEL1 0.15 112
C311 CTL2 -0.18 113
H11X HAL2 0.09 114
H11Y HAL2 0.09 115
C312 CTL2 -0.18 116
H12X HAL2 0.09 117
H12Y HAL2 0.09 118
C313 CTL2 -0.18 119
H13X HAL2 0.09 120
H13Y HAL2 0.09 121
C314 CTL2 -0.18 122
H14X HAL2 0.09 123
H14Y HAL2 0.09 124
C315 CTL2 -0.18 125
H15X HAL2 0.09 126
H15Y HAL2 0.09 127
C316 CTL2 -0.18 128
H16X HAL2 0.09 129
H16Y HAL2 0.09 130
C317 CTL2 -0.18 131
H17X HAL2 0.09 132
H17Y HAL2 0.09 133
C318 CTL3 -0.27 134
H18X HAL3 0.09 135
H18Y HAL3 0.09 136
H18Z HAL3 0.09 137
[ bonds ]
N C11
N C12
N C13
N C14
C11 H11
C11 H12
C11 C15
C12 H21
C12 H22
C12 H23
C13 H31
C13 H32
C13 H33
C14 H41
C14 H42
C14 H43
C15 H51
C15 H52
P1 O1
P1 O2
P1 O3
P1 O4
O1 C15
O2 C1
C1 HA
C1 HB
C1 C2
C2 HS
C2 C3
C2 O21
C3 HX
C3 HY
C3 O31
O21 C21
C21 C22
C21 O22
C22 H2R
C22 H2S
C22 C23
C23 H3R
C23 H3S
C23 C24
C24 H4R
C24 H4S
C24 C25
C25 H5R
C25 H5S
C25 C26
C26 H6R
C26 H6S
C26 C27
C27 H7R
C27 H7S
C27 C28
C28 H8R
C28 H8S
C28 C29
C29 H91
C29 C210
C210 H101
C210 C211
C211 H11R
C211 H11S
C211 C212
C212 H12R
C212 H12S
C212 C213
C213 H13R
C213 H13S
C213 C214
C214 H14R
C214 H14S
C214 C215
C215 H15R
C215 H15S
C215 C216
C216 H16R
C216 H16S
C216 C217
C217 H17R
C217 H17S
C217 C218
C218 H18R
C218 H18S
C218 H18T
O31 C31
C31 C32
C31 O32
C32 H2X
C32 H2Y
C32 C33
C33 H3X
C33 H3Y
C33 C34
C34 H4X
C34 H4Y
C34 C35
C35 H5X
C35 H5Y
C35 C36
C36 H6X
C36 H6Y
C36 C37
C37 H7X
C37 H7Y
C37 C38
C38 H8X
C38 H8Y
C38 C39
C39 H92
C39 C310
C310 H102
C310 C311
C311 H11X
C311 H11Y
C311 C312
C312 H12X
C312 H12Y
C312 C313
C313 H13X
C313 H13Y
C313 C314
C314 H14X
C314 H14Y
C314 C315
C315 H15X
C315 H15Y
C315 C316
C316 H16X
C316 H16Y
C316 C317
C317 H17X
C317 H17Y
C317 C318
C318 H18X
C318 H18Y
C318 H18Z
[ impropers ]
C21 O21 C22 O22
C31 O31 C32 O32
--
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