-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathmartini_v3.0.0_nucleobases_v1.itp
216 lines (169 loc) · 5.59 KB
/
martini_v3.0.0_nucleobases_v1.itp
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
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
;;;;; Martini 3 - Database of nucleobases.
;;;;;
;;;;; File updated on 2021-03-29
;;;;;
;;;;; Version: 3.0.0_v1
;;;;;
;;;;; This collection contains the models included as part of the Martini 3 publication:
;;;;; PCT Souza, et al., Nat. Methods, 2021. DOI: 10.1038/s41592-021-01098-3
; Adenine Martini itp
[ moleculetype ]
; Name nrexcl
ADEN 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SN1 1 ADEN N1 1 0 45.0
2 TN3a 1 ADEN N2 2 0 45.0
3 TN5a 1 ADEN N3 3 0 0.0
4 TP1d 1 ADEN N4 4 0 45.0
5 TN3a 1 ADEN N5 5 0 45.0
6 TC6 1 ADEN N6 6 0 0.0
[constraints]
; i j funct length
1 2 1 0.268
1 5 1 0.287
4 5 1 0.316
2 5 1 0.353
2 4 1 0.417
[ dihedrals ]
; i j k l funct angle force.c
1 2 5 4 2 180.0 400.0
[ virtual_sites3 ]
; VS beads 3fd
; Site from funct a d
3 5 2 4 2 0.52 0.373
[ virtual_sitesn ]
; VS beads in the centre of the mass
; site funct constructing atom indices
6 2 2 5
[ exclusions ]
1 2 3 4 5 6
2 3 4 5 6
3 4 5 6
4 5 6
5 6
; Cytosine Martini itp
[ moleculetype ]
; Name nrexcl
CYTO 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SN1 1 CYTO N1 1 0 45.0
2 TP1a 1 CYTO N2 2 0 45.0
3 TN5a 1 CYTO N3 3 0 0.0
4 TP1d 1 CYTO N4 4 0 45.0
[ bonds ]
; i j funct length force_k
[constraints]
; i j funct length
1 2 1 0.255
1 4 1 0.340
2 4 1 0.412
[angles]
; i j k funct angle force.c.
[dihedrals]
; i j k l funct angle force.c
[ virtual_sitesn ]
; VS beads in the centre of the mass
; site funct constructing atom indices
3 2 2 4
[ exclusions ]
1 2 3 4
2 3 4
3 4
; Guanine Martini itp
[ moleculetype ]
; Name nrexcl
GUAN 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SN1 1 GUAN N1 1 0 45.0
2 TP1d 1 GUAN N2 2 0 45.0
3 TP1d 1 GUAN N3 3 0 0.0
4 TP1a 1 GUAN N4 4 0 45.0
5 TN5a 1 GUAN N5 5 0 0.0
6 TN3a 1 GUAN N6 6 0 0.0
[constraints]
; i j funct length
1 2 1 0.566 100000
1 4 1 0.483 100000
2 4 1 0.504 100000
[ virtual_sitesn ]
; VS beads in the centre of the mass
; site funct constructing atom indices
3 2 2 4
5 2 1 2
6 2 1 1 2 4 4
[ exclusions ]
1 2 3 4 5 6
2 3 4 5 6
3 4 5 6
4 5 6
5 6
; Thymine Martini itp
[ moleculetype ]
; Name nrexcl
THYM 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SN1 1 THYM N1 1 0 45.0
2 TP1a 1 THYM N2 2 0 45.0
3 TN5d 1 THYM N3 3 0 0.0
4 TP1a 1 THYM N4 4 0 45.0
5 TC2 1 THYM N5 5 0 45.0
[ bonds ]
; i j funct length force_k
[constraints]
; i j funct length
1 2 1 0.286 100000
1 4 1 0.371 100000
1 5 1 0.244 100000
2 4 1 0.449 100000
4 5 1 0.251 100000
[ angles ]
; i j k funct angle force.c.
[ dihedrals ]
; i j k l funct angle force.c
1 2 4 5 2 0.0 100.0
[ virtual_sitesn ]
; VS beads in the centre of the mass
; site funct constructing atom indices
3 2 2 4
[ exclusions ]
1 2 3 4 5
2 3 4 5
3 4 5
4 5
; Uracil Martini itp
[ moleculetype ]
; Name nrexcl
URAC 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SN1 1 URAC N1 1 0 45.0
2 TP1a 1 URAC N2 2 0 45.0
3 TN5d 1 URAC N3 3 0 0.0
4 TP1a 1 URAC N4 4 0 45.0
5 TC5 1 URAC N5 5 0 0.0
[ bonds ]
; i j funct length force_k
[constraints]
; i j funct length
1 2 1 0.290
1 4 1 0.374
2 4 1 0.451
[ angles ]
; i j k funct angle force.c.
[ dihedrals ]
; i j k l funct angle force.c
1 2 4 5 2 0.0 100.0
[ virtual_sitesn ]
; VS beads in the centre of the mass
; site funct constructing atom indices
3 2 2 4
5 2 1 4
[ exclusions ]
1 2 3 4 5
2 3 4 5
3 4 5
4 5