Hello all,
I am trying to use the nastruct command to calculate the basic nucleic acids structure parameters of 500 frame MD simulation of a 32bp RNA.
The RNA has 3 consecutive G-U base pairs (2 of them; r10 - r13 & 20 - 22)
However the:
BP.data output
BPstep.data output
Helix.data output
all do not capture parameters for the G-U bps. They are missing from all the output files.
For example::::
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BP.data output>>>>
#Frame Base1 Base2 Shear Stretch Stagger Buckle Propeller Opening BP HB Major Minor
1 1 64 -0.4832 -0.1082 -0.9687 -15.6349 -10.2136 6.3749 1 2 0.0000 12.8730
1 3 62 0.0638 -0.2095 -0.4135 1.3191 -13.8867 0.2925 1 2 18.6218 13.2438
1 4 61 -2.2295 -0.4624 -0.7918 -8.9326 -8.1879 0.5222 1 0 18.8094 13.1070
1 5 60 -0.3302 -0.2089 -0.6546 2.7610 -18.5153 3.1471 1 2 18.1348 13.2356
1 6 59 -0.3048 -0.2837 -0.3637 -8.9297 -26.2722 -3.6968 1 2 18.0371 13.3502
1 8 57 0.3137 0.2243 -0.0599 -6.5792 -19.9784 -1.2544 1 2 18.5768 13.6837
1 9 56 -0.5400 -0.2885 -0.5400 -7.2689 -27.7735 5.3289 1 2 19.2228 13.1121
1 10 55 -0.6456 -0.1005 0.0359 -0.3315 -12.2037 1.4471 1 2 18.7792 13.1521
1 14 51 -0.2762 -0.0595 -0.5191 7.6241 -12.9440 5.3462 1 2 17.8080 12.9903
1 15 50 -0.3271 -0.0187 -0.0433 6.1429 -9.8041 -1.4565 1 2 18.7425 13.3373
1 16 49 -0.4485 0.0501 0.2836 0.5355 -26.4200 0.3466 1 2 18.6483 13.4823
1 17 48 0.3290 -0.0690 -0.2244 12.0882 -12.8594 -8.0159 1 2 19.0141 13.5715
1 18 47 -0.0027 0.0529 -0.1665 11.8541 -15.7696 -6.3387 1 2 19.0966 13.7739
1 19 46 0.1562 -0.2418 -0.2478 3.7666 -14.6892 -7.3291 1 2 19.0988 13.4367
1 23 42 0.2627 -0.2000 0.0622 1.1059 -17.4875 2.8912 1 2 18.5022 13.2493
1 24 41 -0.1175 0.1040 0.0357 15.3664 -13.0139 -2.4185 1 2 19.0036 13.5276
1 25 40 -0.2909 0.0426 -1.0420 1.9853 -15.2294 -6.8545 1 2 18.5646 13.8401
1 26 39 2.4061 -0.4811 0.1010 -7.8567 -4.3681 -2.6702 1 0 18.7721 13.3510
1 27 38 0.6371 -0.2655 0.4360 -6.1555 -26.0192 3.3963 1 2 18.5033 13.0686
1 28 37 -0.5413 0.0441 0.5382 -11.9264 -8.1874 -0.6754 1 2 18.9065 13.4171
1 30 35 -0.2289 -0.1010 -0.0631 9.0915 -20.7575 -4.0550 1 2 18.6153 13.3173
1 32 33 0.1497 -0.1335 -0.8615 23.7854 -0.0932 -4.2117 1 2 0.0000 13.1655
BPstep.data >>>>>
#Frame BP1 BP2 Shift Slide Rise Tilt Roll Twist Zp
1 3-62 4-61 0.0402 -1.7214 3.5308 -2.5007 18.5521 22.5693 2.2531
1 4-61 5-60 -0.1373 -0.8283 3.1520 -0.1434 -0.4697 38.4905 1.6831
1 5-60 6-59 -0.5308 -1.3366 3.7516 -1.4557 9.4965 30.4493 1.8290
1 8-57 9-56 0.1854 -1.6519 3.1651 -0.4340 14.9028 24.5630 1.7648
1 9-56 10-55 -0.3693 -1.0034 3.0934 -9.3717 1.3637 30.7933 1.5218
1 14-51 15-50 -0.3448 -1.3100 3.3673 -3.1108 5.8653 29.8582 1.9989
1 15-50 16-49 0.0038 -1.5166 3.6094 0.1930 8.3076 30.9787 2.2930
1 16-49 17-48 -0.3435 -1.6561 3.1323 2.0181 -1.5892 33.0590 2.1646
1 17-48 18-47 0.1705 -1.4718 3.3020 -0.4148 5.4302 30.2123 2.1324
1 18-47 19-46 0.2729 -1.5393 3.3076 1.5768 10.4283 34.1903 2.2901
1 23-42 24-41 -0.1093 -1.2908 2.9998 -3.6563 -0.3943 26.5696 1.9488
1 24-41 25-40 -0.3565 -1.9514 3.5837 4.1189 17.5067 33.4989 2.4009
1 25-40 26-39 0.4879 -1.5235 3.7774 -3.8317 9.4198 40.9708 2.5030
1 26-39 27-38 0.8703 -2.0451 3.1773 7.0955 1.8546 27.4810 2.5415
1 27-38 28-37 0.3077 -1.9083 3.4491 2.8501 8.8518 26.4984 2.7392
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My cpptraj input looks like the following:
>>>>>>>>>>>>>>>>>>>>>>>
parm pmaa.top
trajin step5_1.xtc
nastruct naout data_32mer_only
>>>>>>>>>>>>>>>>>>>>>>>
Please is there a way to address an issue like this? Any pointers from you are greatly appreciated?
Best wishes,
Francis
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Received on Thu May 13 2021 - 16:00:02 PDT
