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comparison alchemical_run/test-data/morph.top @ 0:5f136e371f44 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit 4c75f8d26505d221d4144f4ae7d2fb7698fbe4ab"
author chemteam
date Mon, 18 Nov 2019 09:52:20 -0500
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comparison
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-1:000000000000 0:5f136e371f44
1 ; Gromacs Topology File written by Sire
2 ; File written 05/01/19 13:21:14
3 [ defaults ]
4 ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
5 1 2 yes 0.5 0.833333
6
7 [ atomtypes ]
8 ; name at.num mass charge ptype sigma epsilon
9 Cl- 17 35.453000 0.000000 A 0.447766 0.148913
10 HW 1 1.007940 0.000000 A 0.000000 0.000000
11 Na+ 11 22.989770 0.000000 A 0.243928 0.365846
12 OW 8 15.999400 0.000000 A 0.315075 0.635968
13 c3 6 12.010700 0.000000 A 0.339771 0.451035
14 ca 6 12.010700 0.000000 A 0.331521 0.413379
15 ha 1 1.007940 0.000000 A 0.262548 0.067362
16 hc 1 1.007940 0.000000 A 0.260018 0.087027
17 hc_du 0 0.000000 0.000000 A 0.000000 0.000000
18
19 [ moleculetype ]
20 ; name nrexcl
21 CL 3
22
23 [ atoms ]
24 ; nr type resnr residue atom cgnr charge mass
25 1 Cl- 1 CL CL 1 -1.000000 35.450000
26
27
28 [ moleculetype ]
29 ; name nrexcl
30 Merged_Molecule 3
31
32 [ atoms ]
33 ; nr type0 resnr residue atom cgnr charge0 mass0 type1 charge1 mass1
34 1 ca 1 LIG C 1 -0.130000 12.010000 ca -0.075744 12.010000
35 2 ca 1 LIG C1 2 -0.130000 12.010000 ca -0.129444 12.010000
36 3 ca 1 LIG C2 3 -0.130000 12.010000 ca -0.131444 12.010000
37 4 ca 1 LIG C3 4 -0.130000 12.010000 ca -0.131444 12.010000
38 5 ca 1 LIG C4 5 -0.130000 12.010000 ca -0.129444 12.010000
39 6 ca 1 LIG C5 6 -0.130000 12.010000 ca -0.075744 12.010000
40 7 ha 1 LIG H 7 0.130000 1.008000 c3 -0.053744 12.010000
41 8 ha 1 LIG H1 8 0.130000 1.008000 ha 0.129056 1.008000
42 9 ha 1 LIG H2 9 0.130000 1.008000 ha 0.130056 1.008000
43 10 ha 1 LIG H3 10 0.130000 1.008000 ha 0.130056 1.008000
44 11 ha 1 LIG H4 11 0.130000 1.008000 ha 0.129056 1.008000
45 12 ha 1 LIG H5 12 0.130000 1.008000 c3 -0.053744 12.010000
46 13 hc_du 1 LIG H 13 0.000000 1.008000 hc 0.043756 1.008000
47 14 hc_du 1 LIG H1 14 0.000000 1.008000 hc 0.043756 1.008000
48 15 hc_du 1 LIG H2 15 0.000000 1.008000 hc 0.043756 1.008000
49 16 hc_du 1 LIG H7 16 0.000000 1.008000 hc 0.043756 1.008000
50 17 hc_du 1 LIG H8 17 0.000000 1.008000 hc 0.043756 1.008000
51 18 hc_du 1 LIG H9 18 0.000000 1.008000 hc 0.043756 1.008000
52
53 [ bonds ]
54 ; ai aj funct parameters
55 1 2 1 0.1398 316812 0.1398 316812
56 1 6 1 0.1398 316812 0.1398 316812
57 1 7 1 0.1086 331122 0.1516 209451
58 2 3 1 0.1398 316812 0.1398 316812
59 2 8 1 0.1086 331122 0.1086 331122
60 3 4 1 0.1398 316812 0.1398 316812
61 3 9 1 0.1086 331122 0.1086 331122
62 4 5 1 0.1398 316812 0.1398 316812
63 4 10 1 0.1086 331122 0.1086 331122
64 5 6 1 0.1398 316812 0.1398 316812
65 5 11 1 0.1086 331122 0.1086 331122
66 6 12 1 0.1086 331122 0.1516 209451
67 7 13 1 0.1097 314553 0.1097 314553
68 7 14 1 0.1097 314553 0.1097 314553
69 7 15 1 0.1097 314553 0.1097 314553
70 12 16 1 0.1097 314553 0.1097 314553
71 12 17 1 0.1097 314553 0.1097 314553
72 12 18 1 0.1097 314553 0.1097 314553
73
74 [ pairs ]
75 ; ai aj funct
76 1 4 1
77 1 9 1
78 1 11 1
79 1 16 1
80 1 17 1
81 1 18 1
82 2 5 1
83 2 10 1
84 2 12 1
85 2 13 1
86 2 14 1
87 2 15 1
88 3 6 1
89 3 7 1
90 3 11 1
91 4 8 1
92 4 12 1
93 5 7 1
94 5 9 1
95 5 16 1
96 5 17 1
97 5 18 1
98 6 8 1
99 6 10 1
100 6 13 1
101 6 14 1
102 6 15 1
103 7 8 1
104 7 12 1
105 8 9 1
106 9 10 1
107 10 11 1
108 11 12 1
109
110 [ angles ]
111 ; ai aj ak funct parameters
112 1 2 3 1 120.02 575.718 120.02 575.718
113 1 2 8 1 119.88 407.522 119.88 407.522
114 1 6 5 1 120.02 575.718 120.02 575.718
115 1 6 12 1 119.88 407.522 120.77 548.941
116 1 7 13 1 110.47 395.806 110.47 395.806
117 1 7 14 1 110.47 395.806 110.47 395.806
118 1 7 15 1 110.47 395.806 110.47 395.806
119 2 1 6 1 120.02 575.718 120.02 575.718
120 2 1 7 1 119.88 407.522 120.77 548.941
121 2 3 4 1 120.02 575.718 120.02 575.718
122 2 3 9 1 119.88 407.522 119.88 407.522
123 3 2 8 1 119.88 407.522 119.88 407.522
124 3 4 5 1 120.02 575.718 120.02 575.718
125 3 4 10 1 119.88 407.522 119.88 407.522
126 4 3 9 1 119.88 407.522 119.88 407.522
127 4 5 6 1 120.02 575.718 120.02 575.718
128 4 5 11 1 119.88 407.522 119.88 407.522
129 5 4 10 1 119.88 407.522 119.88 407.522
130 5 6 12 1 119.88 407.522 120.77 548.941
131 6 1 7 1 119.88 407.522 120.77 548.941
132 6 5 11 1 119.88 407.522 119.88 407.522
133 6 12 16 1 110.47 395.806 110.47 395.806
134 6 12 17 1 110.47 395.806 110.47 395.806
135 6 12 18 1 110.47 395.806 110.47 395.806
136 13 7 14 1 107.58 326.352 107.58 326.352
137 13 7 15 1 107.58 326.352 107.58 326.352
138 14 7 15 1 107.58 326.352 107.58 326.352
139 16 12 17 1 107.58 326.352 107.58 326.352
140 16 12 18 1 107.58 326.352 107.58 326.352
141 17 12 18 1 107.58 326.352 107.58 326.352
142
143 [ dihedrals ]
144 ; ai aj ak al funct parameters
145 1 2 3 4 1 180 15.167 2 180 15.167 2
146 1 2 3 9 1 180 15.167 2 180 15.167 2
147 1 3 2 8 4 180 4.6024 2 180 4.6024 2
148 1 5 6 12 4 180 4.6024 2 0 0 2
149 1 6 5 4 1 180 15.167 2 180 15.167 2
150 1 6 5 11 1 180 15.167 2 180 15.167 2
151 1 6 12 16 1 0 0 0 0 0 0
152 1 6 12 17 1 0 0 0 0 0 0
153 1 6 12 18 1 0 0 0 0 0 0
154 2 1 6 5 1 180 15.167 2 180 15.167 2
155 2 1 6 12 1 180 15.167 2 180 15.167 2
156 2 1 7 13 1 0 0 0 0 0 0
157 2 1 7 14 1 0 0 0 0 0 0
158 2 1 7 15 1 0 0 0 0 0 0
159 2 3 4 5 1 180 15.167 2 180 15.167 2
160 2 3 4 10 1 180 15.167 2 180 15.167 2
161 2 4 3 9 4 180 4.6024 2 180 4.6024 2
162 2 6 1 7 4 180 4.6024 2 180 4.6024 2
163 3 2 1 6 1 180 15.167 2 180 15.167 2
164 3 2 1 7 1 180 15.167 2 180 15.167 2
165 3 4 5 6 1 180 15.167 2 180 15.167 2
166 3 4 5 11 1 180 15.167 2 180 15.167 2
167 3 5 4 10 4 180 4.6024 2 180 4.6024 2
168 4 3 2 8 1 180 15.167 2 180 15.167 2
169 4 5 6 12 1 180 15.167 2 180 15.167 2
170 4 6 5 11 4 180 4.6024 2 180 4.6024 2
171 5 4 3 9 1 180 15.167 2 180 15.167 2
172 5 6 1 7 1 180 15.167 2 180 15.167 2
173 5 6 1 12 4 0 0 2 180 4.6024 2
174 5 6 12 16 1 0 0 0 0 0 0
175 5 6 12 17 1 0 0 0 0 0 0
176 5 6 12 18 1 0 0 0 0 0 0
177 6 1 2 8 1 180 15.167 2 180 15.167 2
178 6 1 7 13 1 0 0 0 0 0 0
179 6 1 7 14 1 0 0 0 0 0 0
180 6 1 7 15 1 0 0 0 0 0 0
181 6 5 4 10 1 180 15.167 2 180 15.167 2
182 7 1 2 8 1 180 15.167 2 180 15.167 2
183 7 1 6 12 1 180 15.167 2 180 15.167 2
184 8 2 3 9 1 180 15.167 2 180 15.167 2
185 9 3 4 10 1 180 15.167 2 180 15.167 2
186 10 4 5 11 1 180 15.167 2 180 15.167 2
187 11 5 6 12 1 180 15.167 2 180 15.167 2
188
189
190 [ moleculetype ]
191 ; name nrexcl
192 NA 3
193
194 [ atoms ]
195 ; nr type resnr residue atom cgnr charge mass
196 1 Na+ 1 NA NA 1 1.000000 22.990000
197
198
199 [ moleculetype ]
200 ; name nrexcl
201 WAT 3
202
203 [ atoms ]
204 ; nr type resnr residue atom cgnr charge mass
205 1 OW 1 WAT O 1 -0.834000 16.000000
206 2 HW 1 WAT H1 2 0.417000 1.008000
207 3 HW 1 WAT H2 3 0.417000 1.008000
208
209 #ifdef FLEXIBLE
210 #else
211
212 [ settles ]
213 ; OW funct doh dhh
214 1 1 0.09572 0.15136
215
216 [ exclusions ]
217 1 2 3
218 2 1 3
219 3 1 2
220
221 #endif
222
223 [ system ]
224 BioSimSpace System
225
226 [ molecules ]
227 ;molecule name nr.
228 Merged_Molecule 1
229 NA 5
230 CL 5
231 WAT 2151
232