Hi Dan,
My system has a protein in a mixed solvent (water+acetonitrile) I have 230 acetonitrile molecules in ~4000 TIP3P waters and my protein
I have been trying to find out binding unbinding events from my 10 independent runs (50- ns each of production), there are 4 spots which have high ACN densities as studied from teh grid command in cpptraj and thus I am trying to study the interactions of ACN molecules with those regions.
You had suggested to use nativecontacts for this purpose and hence mys cript
parm ../run_1/ACN_IL1B_solvated.prmtop
trajin ../run_1/prod/ACN_IL1B_production4A.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4B.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4C.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4D.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4E.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4F.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4G.mdcrd 1 1250 1
trajin ../run_1/prod/ACN_IL1B_production4H.mdcrd 1 1250 1
autoimage
trajin ../run_2/prod/ACN_IL1B_production4A.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4B.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4C.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4D.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4E.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4F.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4G.mdcrd 1 1250 1
trajin ../run_2/prod/ACN_IL1B_production4H.mdcrd 1 1250 1
autoimage
trajin ../run_3/prod/ACN_IL1B_production4A.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4B.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4C.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4D.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4E.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4F.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4G.mdcrd 1 1250 1
trajin ../run_3/prod/ACN_IL1B_production4H.mdcrd 1 1250 1
autoimage
trajin ../run_4/prod/ACN_IL1B_production4A.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4B.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4C.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4D.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4E.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4F.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4G.mdcrd 1 1250 1
trajin ../run_4/prod/ACN_IL1B_production4H.mdcrd 1 1250 1
autoimage
trajin ../run_5/prod/ACN_IL1B_production4A.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4B.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4C.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4D.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4E.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4F.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4G.mdcrd 1 1250 1
trajin ../run_5/prod/ACN_IL1B_production4H.mdcrd 1 1250 1
autoimage
strip :WAT
reference ../run_1/ACN_IL1B_allmin.rst
nativecontacts .N1 .CA,C,N,O,H writecontacts nativecontacts.dat skipnative distance 3.0 out contacts.out first contactpdb contacts.pdb series seriesout native_series.dat savenonnative seriesnnout nn.dat nncontactpdb nn_contact.pdb
go
I have a file nativecontacts.dat the contents of which are as follows: (first 100 lines are pasted here as an example)
# Contacts: Contacts_00002
# Native contacts determined from mask '.N1' and mask '.CA,C,N,O,H'
# Non-native Contacts: Contacts_00002
# Contact Nframes Frac. Avg Stdev
1 :363.N1_:96.H 6401 0.128 2.19 0.205
2 :216.N1_:96.H 4843 0.0969 2.16 0.197
3 :280.N1_:96.H 4602 0.092 2.18 0.203
4 :352.N1_:26.H 3783 0.0757 2.27 0.253
5 :277.N1_:96.H 3217 0.0643 2.17 0.192
6 :324.N1_:80.H 2991 0.0598 2.17 0.198
7 :306.N1_:96.H 2981 0.0596 2.17 0.201
8 :324.N1_:134.H 2932 0.0586 2.21 0.234
9 :169.N1_:24.H 1571 0.0314 2.25 0.243
10 :363.N1_:96.N 1488 0.0298 2.93 0.052
11 :356.N1_:127.H 1456 0.0291 2.31 0.24
12 :347.N1_:66.H 1328 0.0266 2.33 0.261
13 :216.N1_:96.N 1244 0.0249 2.93 0.0524
14 :342.N1_:96.H 1231 0.0246 2.16 0.186
15 :347.N1_:64.H 1114 0.0223 2.52 0.318
16 :280.N1_:96.N 1061 0.0212 2.93 0.053
17 :356.N1_:98.H 997 0.0199 2.23 0.218
18 :290.N1_:26.H 985 0.0197 2.24 0.255
19 :299.N1_:41.H 949 0.019 2.29 0.251
20 :242.N1_:41.H 930 0.0186 2.35 0.257
21 :180.N1_:3.H 832 0.0166 2.3 0.246
22 :363.N1_:86.H 828 0.0166 2.27 0.254
23 :330.N1_:55.H 794 0.0159 2.42 0.279
24 :212.N1_:41.H 788 0.0158 2.3 0.264
25 :277.N1_:96.N 782 0.0156 2.93 0.0534
26 :352.N1_:26.N 762 0.0152 2.93 0.0527
27 :306.N1_:96.N 746 0.0149 2.93 0.0517
28 :208.N1_:66.H 738 0.0148 2.4 0.293
29 :324.N1_:134.N 736 0.0147 2.93 0.0524
30 :324.N1_:80.N 730 0.0146 2.92 0.0558
31 :174.N1_:24.H 705 0.0141 2.23 0.235
32 :316.N1_:7.H 597 0.0119 2.21 0.221
33 :180.N1_:24.H 570 0.0114 2.26 0.262
34 :181.N1_:98.H 562 0.0112 2.33 0.25
35 :240.N1_:94.H 559 0.0112 2.25 0.237
36 :349.N1_:64.H 555 0.0111 2.39 0.318
37 :312.N1_:137.H 555 0.0111 2.41 0.276
38 :177.N1_:7.H 550 0.011 2.24 0.226
39 :226.N1_:41.H 535 0.0107 2.29 0.263
40 :208.N1_:64.H 498 0.00996 2.52 0.315
41 :265.N1_:24.H 482 0.00964 2.25 0.252
42 :326.N1_:138.H 474 0.00948 2.21 0.231
43 :324.N1_:94.H 465 0.0093 2.34 0.256
44 :315.N1_:24.H 457 0.00914 2.23 0.234
45 :194.N1_:41.H 453 0.00906 2.34 0.257
46 :300.N1_:76.H 435 0.0087 2.23 0.235
47 :272.N1_:26.H 423 0.00846 2.35 0.267
48 :349.N1_:66.H 423 0.00846 2.49 0.28
49 :208.N1_:67.H 421 0.00842 2.34 0.285
50 :312.N1_:136.H 421 0.00842 2.63 0.243
51 :347.N1_:7.H 411 0.00822 2.24 0.236
52 :281.N1_:24.H 400 0.008 2.22 0.238
53 :184.N1_:84.H 399 0.00798 2.29 0.302
54 :186.N1_:82.H 399 0.00798 2.39 0.305
55 :169.N1_:24.N 390 0.0078 2.92 0.0555
56 :308.N1_:24.H 388 0.00776 2.26 0.26
57 :191.N1_:84.H 383 0.00766 2.18 0.216
58 :308.N1_:86.H 376 0.00752 2.25 0.221
59 :222.N1_:80.H 367 0.00734 2.15 0.192
60 :238.N1_:84.H 362 0.00724 2.21 0.249
61 :237.N1_:3.H 360 0.0072 2.32 0.259
62 :222.N1_:134.H 359 0.00718 2.21 0.22
63 :231.N1_:24.H 356 0.00712 2.23 0.24
64 :177.N1_:3.H 347 0.00694 2.3 0.283
65 :363.N1_:84.H 343 0.00686 2.2 0.243
66 :202.N1_:24.H 343 0.00686 2.24 0.237
67 :218.N1_:41.H 341 0.00682 2.27 0.249
68 :342.N1_:96.N 333 0.00666 2.93 0.0557
69 :329.N1_:41.H 331 0.00662 2.24 0.232
70 :246.N1_:108.H 329 0.00658 2.17 0.219
71 :204.N1_:24.H 328 0.00656 2.28 0.259
72 :295.N1_:4.H 324 0.00648 2.32 0.27
73 :240.N1_:93.H 317 0.00634 2.7 0.252
74 :367.N1_:41.H 315 0.0063 2.25 0.242
75 :238.N1_:86.H 307 0.00614 2.25 0.254
76 :259.N1_:26.H 307 0.00614 2.35 0.279
77 :347.N1_:66.N 303 0.00606 2.92 0.0547
78 :192.N1_:84.H 298 0.00596 2.25 0.25
79 :338.N1_:76.H 296 0.00592 2.24 0.236
80 :366.N1_:76.H 292 0.00584 2.19 0.218
81 :189.N1_:3.H 290 0.0058 2.28 0.267
82 :189.N1_:76.H 287 0.00574 2.22 0.218
83 :191.N1_:82.H 285 0.0057 2.26 0.247
84 :356.N1_:97.H 285 0.0057 2.84 0.127
85 :295.N1_:108.H 280 0.0056 2.19 0.228
86 :352.N1_:24.H 278 0.00556 2.22 0.259
87 :345.N1_:98.H 276 0.00552 2.34 0.258
88 :240.N1_:84.H 274 0.00548 2.22 0.242
89 :367.N1_:86.H 273 0.00546 2.36 0.281
90 :272.N1_:61.H 272 0.00544 2.3 0.253
91 :356.N1_:98.N 271 0.00542 2.93 0.0568
92 :170.N1_:66.H 269 0.00538 2.25 0.235
93 :202.N1_:64.H 265 0.0053 2.3 0.291
94 :290.N1_:26.N 261 0.00522 2.92 0.0591
95 :354.N1_:24.H 260 0.0052 2.26 0.265
96 :347.N1_:65.H 257 0.00514 2.78 0.177
97 :271.N1_:41.H 256 0.00512 2.23 0.227
98 :330.N1_:54.H 255 0.0051 2.66 0.255
99 :316.N1_:24.H 252 0.00504 2.21 0.239
100 :216.N1_:66.H 252 0.00504 2.45 0.264
101 :300.N1_:75.H 250 0.005 2.66 0.235
102 :322.N1_:66.H 245 0.0049 2.26 0.223
103 :285.N1_:76.H 242 0.00484 2.26 0.225
104 :171.N1_:11.H 242 0.00484 2.74 0.185
105 :293.N1_:66.H 239 0.00478 2.33 0.254
106 :357.N1_:148.H 237 0.00474 2.13 0.197
107 :348.N1_:32.H 237 0.00474 2.35 0.265
What can I infer from this ?
Any idea will help.
Debarati
Postdoctoral research fellow
College of Pharmacy
University of Michigan, USA
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Received on Fri Mar 29 2019 - 11:00:02 PDT
