-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathSLipid_hydrocarbon_topology.dat
190 lines (173 loc) · 4.3 KB
/
SLipid_hydrocarbon_topology.dat
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
!List of parameters for acyl chains
!
!RESI: defines a heavy atom
!
!KEY: ELEMENT LINKER CONNECTIVITY RING BRANCH BOND
! ELEMENT: chemical element (C, N, O, ...)
! LINKER: is it linked to the head group? [0, 1]
! CONNECTIVITY: how many atoms are connected
! RING: Does this belong to a ring? [0, 1]
! BRANCH: does tail branch here? [0, 1]
! BOND: what kind of bond
!
! *: any residue or atom
! &: Improper angle
! -: previous atom
! +: following atom
!HATOM: heavy atom (e.g carbon)
!ATOM: hydrogens
!
!PRES: patch correcting atoms types
!HATOM
!ATOM
!
!Thomas Lemmin
!Laboratory for Biomolecular Modeling, EPFL
!2013
!
!RESI CH0 ! triple bond carbon !No Parameters are currently available
! KEY C 0 2 0 0 3:1
! KEY C 0 2 0 0 1:3
! HATOM C CTL0 -0.09
!ISER
RESI CH1 ! double bond CH1
KEY C 0 2 0 0 2:1
KEY C 0 2 0 0 1:2
KEY C 0 2 0 0 2:-1
KEY C 0 2 0 0 -1:2
HATOM C CEL1 -0.20
ATOM H1 HEL1 0.11
STEREO *:C*+ *:C*- &CH1:C CH1:H1 1.58 110 180 121 1.08
ISER
RESI CH2 ! single bond CH2
KEY C 0 2 0 0 1:1
KEY C 0 2 0 0 1:-1
KEY C 0 2 0 0 -1:1
HATOM C CTL2 0.0
ATOM H1 HAL2 0.0
ATOM H2 HAL2 0.0
STEREO *:C*+ *:C*- &CH2:C CH2:H1 1.53 110 -120 110 1.10
STEREO CH2:H1 *:C*- &CH2:C CH2:H2 1.10 110 -120 110 1.10
ISER
RESI CH3 ! terminal CH3
KEY C 0 1 0 0 1
HATOM C CTL3 -0.081
ATOM H1 HAL3 0.016
ATOM H2 HAL3 0.016
ATOM H3 HAL3 0.016
STEREO *:C*-- *:C*- CH3:C CH3:H1 1.53 110 120 110 1.10
STEREO CH3:H1 *:C*- &CH3:C CH3:H2 1.10 110 120 110 1.10
STEREO CH3:H1 *:C*- &CH3:C CH3:H3 1.10 110 -120 110 1.10
ISER
RESI CH2T ! terminal CH2
KEY C 0 1 0 0 2
HATOM C CGT2 -0.42
ATOM H1 HGT2 0.21
ATOM H2 HGT2 0.21
STEREO *:C*-- *:C*- CH2T:C CH2T:H1 1.53 110 120 110 1.10
STEREO CH3:H1 *:C*- &CH2T:C CH2T:H2 1.10 110 120 110 1.10
ISER
RESI CBH1 ! branched CH1
KEY C 0 3 0 1 1:1:1
HATOM C CTL1 -0.09
ATOM H1 HAL1 0.09
!STEREO *:C*-- *:C*- CBH1:C CBH1:H1 1.53 110 -120 110 1.10
ISER
RESI CRH2 ! cycloprane CH2
KEY C 0 2 1 0 1:1
HATOM C CCP2 -0.18
ATOM H1 HCP2 0.09
ATOM H2 HCP2 0.09
STEREO CRH1:C+ CRH1:C- &CRH2:C CRH2:H1 1.53 110 -112.42 110 1.10
STEREO CRH1:C+ CRH1:C- &CRH2:C CRH2:H2 1.53 110 112.42 110 1.10
ISER
RESI CRH1 ! cycloprane CH1
KEY C 0 3 1 0 1:1:1
KEY C 0 3 1 0 -1:1:1
KEY C 0 3 1 0 1:1:-1
HATOM C CCP1 -0.09
ATOM H1 HCP1 0.09
STEREO CRH2:C+ *:C*- &CRH1:C CRH1:H1 1.53 115 -145 115 1.10
STEREO CRH1:C+ *:C*- &CRH1:C CRH1:H1 1.53 115 145 115 1.10
STEREO *:C*+ CRH1:C- &CRH1:C CRH1:H1 1.53 115 145 115 1.10
STEREO *:C*+ CRH2:C- &CRH1:C CRH1:H1 1.53 115 -145 115 1.10
ISER
RESI CBRH1 ! cycloprane CH1 branch
KEY C 0 3 1 1 1:1:1
HATOM C CCP1 -0.09
ATOM H1 HCP1 0.09
STEREO *:C*+ CRH1:C- &CBRH1:C CBRH1:H1 1.53 115 -145 115 1.10
ISER
PRES CTL2 !correction for trans lipid
CONNECT CTL2 CEL1
HATOM C CTL2 0.03
ATOM H1 HAL2 0.03
ATOM H2 HAL2 0.03
SERP
PRES CTL2 !correction for trans lipid
CONNECT CTL2 CTL3
HATOM C CTL2 0.047
ATOM H1 HAL2 -0.007
ATOM H2 HAL2 -0.007
SERP
BOND
*:C* *:C* 1.52 ! default value C-C
!single bond
CH2:C CH2:C 1.52
!double bond
CH1:C CH1:C 1.35
! triple bond
CH0:C CH0:C 1.20
!cyclopropane
CRH1:C CRH1:C 1.51
CRH1:C CRH2:C 1.51
CRH2:C CRH1:C 1.51
ANGLE
*:C* *:C* *:C* 116
CH2:C CH2:C CH2:C 116
*:C* CH1:C CH1:C 124
CH1:C CH1:C *:C* 124
*:C* CH0:C CH0:C 180
CH0:C CH0:C *:C* 180
*:C* CH1:C CH2:C 120
CH1:C CH2:C *:C* 120
*:C* CBH1:C *:C* 110
!cyclopropane
CRH2:C CRH1:C CRH1:C 60
CRH1:C CRH2:C CRH1:C 60
CRH1:C CRH1:C CRH2:C 60
*:C* CRH1:C CRH2:C 117
*:C* CRH1:C CRH1:C 117
CRH1:C CRH1:C *:C* 117
CRH2:C CRH1:C *:C* 117
!branched cyclopropane
*:C* CRH1:C CBRH1:C 117
CBRH1:C CRH1:C *:C* 117
CRH1:C CBRH1:C *:C* 117
DIHEDRAL
*:C* *:C* *:C* *:C* 180
*:C* CH1:C CH1:C *:C* 180
CH1:C CH1:C *:C* *:C* 130
CH1:C *:C* CH1:C CH1:C 125
*:C* *:C* CH1:C CH1:C 125
CH1:C CH1:C *:C* *:C* 125
*:C* CH2:C CH2:C *:C* 180
*:C* CH2:C CBH1:C *:C* 0 120 240
CH1:C CH1:C CBH1:C *:C* 0 -120 240
*:C* *:C* CBH1:C *:C* -75.36
!*:C* CRH1:C CRH2:C CRH1:C -77.30
!cyclopropane
!*:C* *:C* CRH1:C CRH2:C 120.30 -120.36
*:C* CRH1:C CRH1:C *:C* 0
*:C* CRH2:C CRH1:C *:C* -107
*:C* *:C* CRH1:C CRH1:C 176
CRH1:C CRH1:C *:C* *:C* 176
CRH2:C CRH1:C *:C* *:C* -116
*:C* *:C* CRH1:C CRH2:C 116
!branched cyclopropane
*:C* *:C* CRH1:C CBRH1:C 116
*:C* CRH1:C CRH1:C CBRH1:C -107
*:C* CRH1:C CBRH1:C CRH1:C 107
*:C* CRH1:C CBRH1:C *:C* 0
CRH1:C CRH1:C CBRH1:C *:C* 110
CRH1:C CBRH1:C CRH1:C *:C* -110