Hi,
On Fri, Mar 29, 2019 at 1:50 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
> 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
You don't need to put 'autoimage' after every group of simulations -
it's redundant. The way you have things written cpptraj is doing 5
separate autoimage commands that do the same thing. Also, by default
cpptraj reads in all frames, so if each trajectory is 1250 frames you
can omit the start, stop, and offset arguments Cpptraj does respect
file wildcards, so you can probably get away with:
trajin ../run_?/prod/ACN_IL1B_production*.mdcrd
strip :WAT
autoimage
Placing 'strip' before 'autoimage' makes it so that 'autoimage' has to
do less work since it will have fewer molecules to deal with. You may
want to subsequently repeat the analysis with subsets of the
trajectories to get an idea of your sampling. Also, there's no need to
specify a reference structure.
> 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
OK - so thinking about it more I think what you really might want to
do here is leverage the 'hbond' command (just force it to look for
more than hydrogen bonds) because you don't care about which
acetonitrile is associating with protein, right? So, what I think will
work is:
1) Use 'solventdonor' and 'solventacceptor' to define acetonitrile as
the solvent.
2) Override cpptraj's automatic determination of hydrogen bond
donors/acceptors by specifying only heavy atoms in 'donormask',
'donorhmask', and 'acceptormask'
3) Tell 'hbond' to ignore the angle calculation
4) Ignore intramolecular hydrogen bonds with 'nointramol'
Example (assuming acetonitrile residues are named C3N and the protein
is molecule 1):
hbond donormask ^1&!.H= donorhmask ^1&!.H= acceptormask ^1&!.H= \
solventdonor :C3N.N1 solventacceptor :C3N.N1 \
angle -1 nointramol \
out hbvtime.dat solvout avg.dat
I haven't tested this thoroughly but I'm pretty sure it will work. Let
me know if not.
-Dan
> 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 Sat Mar 30 2019 - 06:30:03 PDT
