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Questions and answers > MD simulations
Analysis of helical parameter of DNA with unnatural
priyabrata das:
We are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, the base pair DX:DY was not be recognized when I used “find_pair”. Notably, the unrecognized base-pair ( DX, DY ) are not typical purine or pyrimidine. How can I analysis the confirmation parameters with 3DNA in such case?
The PDB files of DX, DY, and a frame of MD simulations(XY.pdb) are given in the attachment. Thank you very much!
Thanks and Best wishes
Priyabrata Das
xiangjun:
Hi Priyabrata Das,
Thanks for using 3DNA and reporting the unidentified pairing issue you experienced on the Forum.
The problem is due to DY, which is a special modified case that cannot be properly recognized by 3DNA. More specifically, it is the N7 atom (see the attached image below) that causes the trouble.
I may consider refining the algorithm in 3DNA v2.4 for base identification in special cases like this. For now, simply renaming N7 to NX (for example) would do the trick. Alternatively (and better yet), you may want to give DSSR a try (see below).
Best regards,
Xiang-Jun
PS. The issue is fixed in DSSR v1.8.8, released today. Here is an excerpt of the DSSR output on your structure (XY.pdb).
--- Code: ---List of 4 types of 12 modified nucleotides
nt count list
1 DP-g 4 DP6,DP7,DP22,DP23
2 DZ-c 4 DZ10,DZ11,DZ26,DZ27
3 DP4-g 2 DP4/8,DP4/24
4 DZ5-c 2 DZ5/9,DZ5/25
****************************************************************************
List of 16 base pairs
nt1 nt2 bp name Saenger LW DSSR
1 DC5/1 DG3/32 C-G WC 19-XIX cWW cW-W
2 DT2 DA31 T-A WC 20-XX cWW cW-W
3 DT3 DA30 T-A WC 20-XX cWW cW-W
4 DA4 DT29 A-T WC 20-XX cWW cW-W
5 DT5 DA28 T-A WC 20-XX cWW cW-W
6 DP6 DZ27 g-c WC 19-XIX cWW cW-W
7 DP7 DZ26 g-c WC 19-XIX cWW cW-W
8 DP4/8 DZ5/25 g-c WC 19-XIX cWW cW-W
9 DZ5/9 DP4/24 c-g WC 19-XIX cWW cW-W
10 DZ10 DP23 c-g WC 19-XIX cWW cW-W
11 DZ11 DP22 c-g WC 19-XIX cWW cW-W
12 DA12 DT21 A-T WC 20-XX cWW cW-W
13 DT13 DA20 T-A WC 20-XX cWW cW-W
14 DA14 DT19 A-T WC 20-XX cWW cW-W
15 DA15 DT18 A-T WC 20-XX cWW cW-W
16 DG3/16 DC5/17 G-C WC 19-XIX cWW cW-W
--- End code ---
xiangjun:
As a follow-up, the issue of special base identification has been solved in 3DNA v2.4.2-2019feb26. Using your sample XY.pdb as an example, running find_pair on it would give the following result.
# find_pair XY.pdb
XY.pdb
XY.out
2 # duplex
16 # number of base-pairs
1 1 # explicit bp numbering/hetero atoms
1 32 0 # 1 | ....>-:...1_:[DC5]C-----G[DG3]:..32_:-<.... 0.46 0.40 19.88 9.09 -2.76
2 31 0 # 2 | ....>-:...2_:[.DT]T-----A[.DA]:..31_:-<.... 0.60 0.53 10.04 9.21 -2.83
3 30 0 # 3 | ....>-:...3_:[.DT]T-----A[.DA]:..30_:-<.... 0.36 0.30 17.72 8.87 -3.14
4 29 0 # 4 | ....>-:...4_:[.DA]A-----T[.DT]:..29_:-<.... 0.41 0.40 38.23 8.81 -1.88
5 28 0 # 5 | ....>-:...5_:[.DT]T-----A[.DA]:..28_:-<.... 0.17 0.00 16.14 8.71 -4.02
6 27 0 # 6 | ....>-:...6_:[.DP]g-----c[.DZ]:..27_:-<.... 0.33 0.22 7.19 9.17 -3.87
7 26 0 # 7 | ....>-:...7_:[.DP]g-----c[.DZ]:..26_:-<.... 0.10 0.05 9.70 9.19 -4.31
8 25 0 # 8 | ....>-:...8_:[DP4]g-----c[DZ5]:..25_:-<.... 0.26 0.16 1.36 9.34 -4.36
9 24 0 # 9 | ....>-:...9_:[DZ5]c-----g[DP4]:..24_:-<.... 0.28 0.08 18.81 9.16 -3.62
10 23 0 # 10 | ....>-:..10_:[.DZ]c-----g[.DP]:..23_:-<.... 0.80 0.27 3.53 9.02 -3.48
11 22 0 # 11 | ....>-:..11_:[.DZ]c-----g[.DP]:..22_:-<.... 0.12 0.08 8.89 9.26 -4.27
12 21 0 # 12 | ....>-:..12_:[.DA]A-----T[.DT]:..21_:-<.... 0.46 0.22 23.75 9.24 -0.92
13 20 0 # 13 | ....>-:..13_:[.DT]T-----A[.DA]:..20_:-<.... 0.54 0.39 32.66 9.18 -2.04
14 19 0 # 14 | ....>-:..14_:[.DA]A-----T[.DT]:..19_:-<.... 0.49 0.46 7.28 8.95 -3.22
15 18 0 # 15 | ....>-:..15_:[.DA]A-----T[.DT]:..18_:-<.... 0.91 0.90 18.95 9.13 -1.35
16 17 0 # 16 | ....>-:..16_:[DG3]G-----C[DC5]:..17_:-<.... 0.69 0.64 7.76 9.08 -2.64
##### Base-pair criteria used: 4.00 0.00 15.00 2.50 65.00 4.50 7.80 [ O N]
##### 0 non-Watson-Crick base-pairs, and 1 helix (0 isolated bps)
##### Helix #1 (16): 1 - 16
Best regards,
Xiang-Jun
priyabrata das:
Dear Xiang-Jun,
Thank you very much for your follow up.
Thanks and Regard
Priyabrata Das
priyabrata das:
Dear Xiang-Jun,
Thank you very much for your previous follow up.
One more query I have, when I am running my attached PDB file it shows only 13 base pairs instead of 16 base pairs.
For your reference, I had attached the output file. Kindly suggest, how to find the parameter for all 16 base pair.
Thanks and Regards
Priyabrata Das
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
