3DNA Forum

Questions and answers => MD simulations => Topic started by: priyabrata das on February 18, 2019, 06:09:48 am

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.1 (DSSR Manual) · Homepage

Title: Analysis of helical parameter of DNA with unnatural
Post by: priyabrata das on February 18, 2019, 06:09:48 am
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
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: xiangjun on February 18, 2019, 10:33:13 am
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: [Select]
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
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: xiangjun on February 26, 2019, 11:43:57 am
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
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: priyabrata das on February 26, 2019, 11:56:24 pm
Dear Xiang-Jun,

Thank you very much for your follow up.


Thanks and Regard
Priyabrata Das
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: priyabrata das on February 28, 2019, 01:19:07 am
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
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: xiangjun on February 28, 2019, 11:00:25 am
Dear Priyabrata,

Thanks for your new question regarding the three missing pairs in your 4xno-MY.pdb structure. By attaching both PDB and the 3DNA output files, you've made the issue easy to solve.

The attached 4xno-MY.out contains the following info at the beginning:

****************************************************************************
    3DNA v2.3.4-2018nov06, created and maintained by Xiang-Jun Lu (PhD)
****************************************************************************
1. The list of the parameters given below correspond to the 5' to 3' direction
   of strand I and 3' to 5' direction of strand II.

2. All angular parameters, except for the phase angle of sugar pseudo-
   rotation, are measured in degrees in the range of [-180, +180], and all
   displacements are measured in Angstrom units.
****************************************************************************
File name: 4xno-DP4-md23_rst.pdb
Date and time: Mon Feb 18 16:56:33 2019

Number of base-pairs: 13
Number of atoms: 27438
****************************************************************************


Using 3DNA v2.4.2-2019feb26 would solve the problem. Please have a try and report back how it goes.

Best regards,

Xiang-Jun
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: xiangjun on February 28, 2019, 01:44:39 pm
As a follow-up note to my previous response, you could also try the significantly enhanced web 3DNA 2.0 server at http://web.x3dna.org. It runs on the latest 3DNA distribution.

Xiang-Jun
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: priyabrata das on March 01, 2019, 03:28:43 am
Dear Xiang-Jun

Web 3DNA 2.0 server at http://web.x3dna.org is not been updated to latest version. Now it is running in 3DNA v2.4.1-2019feb11.

Thanks and Regards
Priyabrata Das
Title: Re: Analysis of helical parameter of DNA with unnatural
Post by: xiangjun on March 01, 2019, 08:16:55 am
Did you install 3DNA v2.4.2 and ran it on your structure as suggested?

Or did you upload your structure your structure to web 3DNA 2.0 at the http://web.x3dna.org? Please provide output details on the analysis of your structure, not an output from giving a PDP entry.

Please respond specifically to my queries which are direct related to your questions.

Thanks.

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University