[gmx-users] CHARMM27 topology for DOPC
Peter C. Lai
pcl at uab.edu
Fri Mar 23 22:28:48 CET 2012
Compare and contrast with Klauda et al. Phys Chem. B, 2010, 114, 7830 ?
On 2012-03-23 02:28:45PM -0500, Krzysztof Kuczera wrote:
> 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: kkuczera at 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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--
==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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