Hi,
As pointed out to me by Dr. Christina Bergonzo, G-U base pairing can
be very transient, so you may want to try adding the 'allframes'
keyword to the 'nastruct' command so that cpptraj determines base
pairing each frame instead of based on the first frame.
-Dan
On Thu, May 13, 2021 at 6:49 PM Francis Acquah
<francis.asieduacquah.outlook.com> wrote:
>
> 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::::
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> 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
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 14 2021 - 11:30:02 PDT
