Issue resolved. Changed the reference to calculate base pairing using the
"reference" keyword.
On Wed, Dec 1, 2021 at 4:23 PM Abhilash J <md.scfbio.gmail.com> wrote:
> Hi everyone,
>
> I am trying to calculate DNA base pair parameters using nastruct.
> Cpptraj is unable to recognize one base pair, as shown below in the output.
> The missing base pair can be visualized in trajectory. This input file
> works fine for other DNA runs. Is there something I can do to specify this
> base pair.
> DNA has an insertion at residue 1547 (cpptraj gets that correctly).
>
> Result for first frame
> =======================================
> Frame Base1 Base2 Shear Stretch Stagger Buckle
> Propeller Opening BP HB Major Minor
> 1 1536 1579 0.2332 0.0039 -0.0633 2.1716
> -1.0760 -2.1533 1 3 19.1805 12.8616
> 1 1537 1578 -0.1674 -0.2465 0.2166 4.2907
> -4.9260 -3.2353 1 3 20.1570 12.2788
> 1 1538 1577 0.1294 -0.1372 0.4685 4.8267
> -11.6995 -1.3720 1 2 18.6544 12.4751
> 1 1539 1576 -0.1785 -0.0167 -0.4919 7.4716
> -0.0919 -0.5989 1 3 19.1848 12.2297
> 1 1540 1575 -0.3373 -0.1378 0.2670 8.0676
> -9.7906 3.1343 1 3 18.2930 13.0930
> 1 1541 1574 0.2397 -0.2072 0.7767 -14.6499
> -14.7632 -4.3046 1 3 18.4692 12.3543
> 1 1542 1573 -0.0451 -0.0265 0.9463 -8.8935
> 8.4141 7.3599 1 2 19.7461 11.6316
> 1 1543 1572 0.1219 -0.2388 0.6998 -1.9885
> 0.1273 -7.9407 1 2 19.7073 11.9932
> 1 1544 1571 0.3820 -0.0302 -0.2582 -4.0748
> -0.5055 -3.0481 1 3 18.5288 12.8949
> 1 1545 1570 0.0575 -0.0552 -0.1793 3.5082
> 5.2004 -3.6860 1 3 19.3926 12.8660
> 1 1546 1569 -0.2207 -0.3388 -0.8544 6.9745
> 17.3622 -7.2706 1 3 19.1646 11.5876
> 1 1548 1568 -0.1227 -0.1096 0.3878 -14.9332
> 3.1460 -4.5292 1 3 17.8723 12.3766
> 1 1549 1567 -0.1416 -0.1335 0.1569 -13.0959
> 6.5505 -3.7854 1 3 18.2857 12.0946
> 1 1550 1566 -0.1012 -0.1099 -0.0176 -9.6557
> -16.3165 -3.6273 1 3 19.3297 12.6167
> ===> missing base pair (1551-1565)
> 1 1552 1564 -0.2051 0.0394 -0.4791 0.9259
> -5.0267 1.0486 1 3 19.8023 12.6068
> 1 1553 1563 -0.3255 0.1098 0.2169 17.0099
> -2.0000 4.0067 1 2 20.8265 12.5131
> 1 1554 1562 -0.0609 0.1505 -0.3288 13.8329
> -11.7389 -0.6964 1 3 19.1389 13.2040
> 1 1555 1561 0.1863 -0.0282 -0.2197 -9.9956
> -5.5364 -2.5676 1 3 20.5404 12.4894
> 1 1556 1560 0.2871 0.0177 -0.4274 -6.1873
> -13.5951 -0.0291 1 2 19.4447 12.3209
> 1 1557 1559 0.2874 -0.1365 0.1803 -16.7007
> 11.2121 -5.7795 1 3 19.2165 12.2157
> =======================================
>
> The Input file i used:
> =======================================
> parm ../stripped.complex_wat.prmtop
>
> trajin ../traj1.nc 1 last 100
> trajin ../traj2.nc 1 last 100
>
> rms first :1-530&!.H
>
> nastruct resrange :1536-1557,1559-1579 naout DNA.out
> =======================================
>
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Received on Wed Dec 01 2021 - 17:00:02 PST
