-
Notifications
You must be signed in to change notification settings - Fork 1
/
ala2.prmtop
257 lines (254 loc) · 18.5 KB
/
ala2.prmtop
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
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
%VERSION VERSION_STAMP = V0001.000 DATE = 12/15/20 08:25:04
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 43 24 0 0
99 3 9 11 24 11 21 19 8 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
H1 CH3 H2 H3 C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG ATOMIC_NUMBER
%FORMAT(10I8)
1 6 1 1 6 8 7 1 6 1
6 1 1 1 6 8 7 1 6 1
1 1
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
6 7 4 3 7 3 10 4 10 7
6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 3.17000000E+02 4.34000000E+02 3.37000000E+02 3.40000000E+02
3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.52200000E+00 1.01000000E+00 1.44900000E+00 1.09000000E+00
1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
8.00000000E+01 7.00000000E+01 5.00000000E+01 6.30000000E+01 5.00000000E+01
5.00000000E+01 5.00000000E+01 8.00000000E+01 7.00000000E+01 5.00000000E+01
5.00000000E+01 8.00000000E+01 6.30000000E+01 3.50000000E+01 5.00000000E+01
5.00000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 2.12755727E+00 1.93906163E+00 1.91113635E+00
1.91113635E+00 1.91113635E+00 2.10137732E+00 2.03505478E+00 2.06018753E+00
1.91113635E+00 1.91462701E+00 1.92160833E+00 1.91113635E+00 2.06018753E+00
1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 2.00000000E+00 4.00000000E-01
0.00000000E+00 0.00000000E+00 2.70000000E-01 4.20000000E-01 8.00000000E-01
8.00000000E-02 1.55555556E-01 2.00000000E-01 2.00000000E-01 4.50000000E-01
1.58000000E+00 5.50000000E-01 1.05000000E+01 1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00
3.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00 1.00000000E+00
2.00000000E+00 3.00000000E+00 2.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
%FLAG SCEE_SCALE_FACTOR
%FORMAT(5E16.8)
1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00
1.20000000E+00 1.20000000E+00 0.00000000E+00 0.00000000E+00
%FLAG SCNB_SCALE_FACTOR
%FORMAT(5E16.8)
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00
2.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 8 54 57 10 54 60 10
54 63 10 48 51 8
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
7 18 24 9 48 54 11
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 10 27 24
42 11 24 30 33 12 24 30 36 12
24 30 39 12 21 18 24 15 18 24
27 16 60 54 63 19 57 54 60 19
57 54 63 19 51 48 54 20 48 54
57 21 48 54 60 21 48 54 63 21
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 8 30 24 42 9 24 42
45 13 24 42 48 14 18 24 30 17
18 24 42 18
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 10
9 3 -12 15 3 9 3 -12 15 11
9 3 12 18 3 6 3 12 15 10
6 3 -12 15 3 6 3 -12 15 11
6 3 12 18 3 3 12 18 21 2
0 3 12 15 10 0 3 -12 15 3
0 3 -12 15 11 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 12
36 30 24 42 12 33 30 24 42 12
27 24 30 33 12 27 24 30 36 12
27 24 30 39 12 27 24 42 45 10
27 24 -42 45 3 27 24 -42 45 11
27 24 42 48 3 24 42 48 51 2
21 18 24 27 3 21 18 24 30 3
21 18 24 42 3 18 24 30 33 12
18 24 30 36 12 18 24 30 39 12
51 48 54 57 3 51 48 54 60 3
51 48 54 63 3 12 24 -18 -21 19
42 54 -48 -51 19
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 1
12 18 -24 30 4 12 18 -24 30 5
12 18 -24 30 6 12 18 24 42 7
12 18 -24 42 8 12 18 -24 42 9
12 18 -24 42 6 3 12 18 24 2
45 42 48 54 2 30 24 42 45 3
30 24 42 48 13 30 24 -42 48 14
30 24 -42 48 5 30 24 -42 48 6
24 42 48 54 2 18 24 42 45 3
18 24 42 48 15 18 24 -42 48 16
18 24 -42 48 17 18 24 -42 48 6
3 18 -12 -15 18 24 48 -42 -45 18
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CX H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
ArgH and AspGluO modified Bondi2 radii (mbondi3)
%FLAG RADII
%FORMAT(5E16.8)
1.20000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.20000000E+00
1.70000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.20000000E+00
1.20000000E+00 1.20000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01
%FLAG IPOL
%FORMAT(1I8)
0