-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathX77A_REAC.nw
282 lines (267 loc) · 7.84 KB
/
X77A_REAC.nw
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
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
title "X77A"
start X77A
echo
charge -1
memory total 1000 mb
#print debug
SCRATCH_DIR /tmp
PERMANENT_DIR .
prepare
directory_3 ../
system X77A
source ./X77A-F.pdb
amber
new_top new_seq
new_rst
modify atom 401:_C1 quantum
modify atom 401:_F1 quantum
modify atom 401:_C2 quantum
modify atom 401:_O2 quantum
modify atom 401:_N3 quantum
modify atom 401:_H3 quantum
modify atom 401:_C4 quantum
modify atom 401:_O4 quantum
modify atom 401:_N5 quantum
modify atom 401:_C6 quantum
modify atom 401:_H6 quantum
modify atom 401:_CZ quantum
modify atom 401:_OZ quantum
modify atom 401:_NY quantum
modify atom 401:_CY quantum
modify atom 401:2HY quantum
modify atom 401:3HY quantum
modify atom 401:_CY1 quantum
modify atom 401:_HY1 quantum
modify atom 401:_CM quantum
modify atom 401:_CM1 quantum
modify atom 401:_HM1 quantum
modify atom 401:_CM2 quantum
modify atom 401:_HM2 quantum
modify atom 401:_CM3 quantum
modify atom 401:_HM3 quantum
modify atom 401:_CM4 quantum
modify atom 401:_HM4 quantum
modify atom 401:_CM5 quantum
modify atom 401:_CN quantum
modify atom 401:_CN1 quantum
modify atom 401:2HN1 quantum
modify atom 401:3HN1 quantum
modify atom 401:4HN1 quantum
modify atom 401:_CN2 quantum
modify atom 401:2HN2 quantum
modify atom 401:3HN2 quantum
modify atom 401:4HN2 quantum
modify atom 401:_CN3 quantum
modify atom 401:2HN3 quantum
modify atom 401:3HN3 quantum
modify atom 401:4HN3 quantum
modify atom 401:_CL quantum
modify atom 401:_CL1 quantum
modify atom 401:_HL1 quantum
modify atom 401:_CL2 quantum
modify atom 401:_HL2 quantum
modify atom 401:_CL3 quantum
modify atom 401:_HL3 quantum
modify atom 401:_NL quantum
modify atom 401:_CL4 quantum
modify atom 401:_HL4 quantum
modify atom 401:_CP quantum
modify atom 401:_OP quantum
modify atom 401:_NP quantum
modify atom 401:_HP quantum
modify atom 401:_CQ quantum
modify atom 401:_HQ quantum
modify atom 401:_CQ1 quantum
modify atom 401:2HQ1 quantum
modify atom 401:3HQ1 quantum
modify atom 401:_CQ2 quantum
modify atom 401:2HQ2 quantum
modify atom 401:3HQ2 quantum
modify atom 401:_CQ3 quantum
modify atom 401:2HQ3 quantum
modify atom 401:3HQ3 quantum
modify atom 401:_CQ4 quantum
modify atom 401:2HQ4 quantum
modify atom 401:3HQ4 quantum
modify atom 401:_CQ5 quantum
modify atom 401:2HQ5 quantum
modify atom 401:3HQ5 quantum
modify atom 25:_CA quantum
modify atom 25:_HA quantum
modify atom 25:_CB quantum
modify atom 25:_HB quantum
modify atom 25:_CG2 quantum
modify atom 25:2HG2 quantum
modify atom 25:3HG2 quantum
modify atom 25:4HG2 quantum
modify atom 25:_OG1 quantum
modify atom 25:_HG1 quantum
modify atom 25:_C quantum
modify atom 25:_O quantum
modify atom 26:_N quantum
modify atom 26:_H quantum
modify atom 26:_CA quantum
modify atom 26:_HA quantum
modify atom 26:_C quantum
modify atom 26:_O quantum
modify atom 27:_N quantum
modify atom 27:_H quantum
modify atom 27:_CA quantum
modify atom 27:_HA quantum
modify atom 41:_CA quantum
modify atom 41:_HA quantum
modify atom 41:_CB quantum
modify atom 41:2HB quantum
modify atom 41:3HB quantum
modify atom 41:_CG quantum
modify atom 41:_ND1 quantum
modify atom 41:_HD1 quantum
modify atom 41:_CD2 quantum
modify atom 41:_HD2 quantum
modify atom 41:_CE1 quantum
modify atom 41:_HE1 quantum
modify atom 41:_NE2 quantum
modify atom 41:_HE2 quantum
modify atom 141:_CA quantum
modify atom 141:_HA quantum
modify atom 141:_C quantum
modify atom 141:_O quantum
modify atom 142:_N quantum
modify atom 142:_H quantum
modify atom 142:_CA quantum
modify atom 142:_HA quantum
modify atom 142:_CB quantum
modify atom 142:2HB quantum
modify atom 142:3HB quantum
modify atom 142:_CG quantum
modify atom 142:_OD1 quantum
modify atom 142:_ND2 quantum
modify atom 142:2HD2 quantum
modify atom 142:3HD2 quantum
modify atom 142:_C quantum
modify atom 142:_O quantum
modify atom 143:_N quantum
modify atom 143:_H quantum
modify atom 143:_CA quantum
modify atom 143:2HA quantum
modify atom 143:3HA quantum
modify atom 143:_C quantum
modify atom 143:_O quantum
modify atom 144:_N quantum
modify atom 144:_H quantum
modify atom 144:_CA quantum
modify atom 144:_HA quantum
modify atom 144:_CB quantum
modify atom 144:2HB quantum
modify atom 144:3HB quantum
modify atom 144:_OG quantum
modify atom 144:_HG quantum
modify atom 144:_C quantum
modify atom 144:_O quantum
modify atom 145:_N quantum
modify atom 145:_H quantum
modify atom 145:_CA quantum
modify atom 145:_HA quantum
modify atom 145:_CB quantum
modify atom 145:2HB quantum
modify atom 145:3HB quantum
modify atom 145:_SG quantum
modify atom 145:_C quantum
modify atom 145:_O quantum
modify atom 146:_N quantum
modify atom 146:_H quantum
modify atom 146:_CA quantum
modify atom 146:2HA quantum
modify atom 146:3HA quantum
modify atom 164:_CA quantum
modify atom 164:_HA quantum
modify atom 164:_CB quantum
modify atom 164:2HB quantum
modify atom 164:3HB quantum
modify atom 164:_CG quantum
modify atom 164:_ND1 quantum
modify atom 164:_CD2 quantum
modify atom 164:_HD2 quantum
modify atom 164:_CE1 quantum
modify atom 164:_HE1 quantum
modify atom 164:_NE2 quantum
modify atom 164:_HE2 quantum
modify atom 164:_C quantum
modify atom 164:_O quantum
modify atom 165:_N quantum
modify atom 165:_H quantum
modify atom 165:_CA quantum
modify atom 165:_HA quantum
modify atom 187:_CA quantum
modify atom 187:_HA quantum
modify atom 187:_CB quantum
modify atom 187:2HB quantum
modify atom 187:3HB quantum
modify atom 187:_CG quantum
modify atom 187:_OD1 quantum
modify atom 187:_OD2 quantum
modify atom 501:2HW quantum
modify atom 501:_OW quantum
modify atom 501:3HW quantum
modify atom 502:2HW quantum
modify atom 502:_OW quantum
modify atom 502:3HW quantum
modify atom 504:2HW quantum
modify atom 504:_OW quantum
modify atom 504:3HW quantum
modify atom 505:2HW quantum
modify atom 505:_OW quantum
modify atom 505:3HW quantum
modify atom 506:2HW quantum
modify atom 506:_OW quantum
modify atom 506:3HW quantum
modify atom 509:2HW quantum
modify atom 509:_OW quantum
modify atom 509:3HW quantum
modify atom 513:2HW quantum
modify atom 513:_OW quantum
modify atom 513:3HW quantum
update lists
ignore
write X77A.rst
write X77A.pdb
end
task prepare
driver
tight
end
md
system X77A
noshake solute
cutoff 10 qmmm 10
msa 30000
end
basis
* library "6-31G*"
end
dft
disp vdw 3
maxiter 250
xc pbe0
direct
grid
end
qmmm
region qmlink mm_solute
method bfgs lbfgs
maxiter 5 100
density espfit
ncycles 50
convergence 1d-7
bqzone 200
end
constraints
# spring bond 175 107 1.0 4.0
end
task qmmm dft optimize
prepare
system X77A
read rst X77A.rst
write solute pdb X77A-F.pdb
end
task prepare