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 - 13:30:02 PST
