How do I build nucleic acid structures with sugar-phosphate backbone?

[xiangjun]

The easiest way to build a nucleic acid structure with the sugar-phosphate backbone, other than predefined fiber models, is to use the rebuild program. The backbone building scheme uses exactly the same protocol as the default for base-only model. The user needs to add the -atomic option to rebuild, and to choose the desired rigid sugar-phosphate backbone to be attached to the standard base geometry.

The four types of currently available backbone conformations are listed in the directory $X3DNA/config/atomic. To use any of these backbones, it is necessary to copy the standard nucleotide files associated with each type of backbone to $X3DNA/config or your current working directory, and to name each nucleotide as follows: Atomic_X.pdb (where X = A, C, G, T, U; or Atomic.x.pdb where x =  a, c, g, t, u for modified bases). The default Atomic_X.pdb files contains only the C1' backbone atom, and the base geometry is independent of the backbone conformation.

To build a DNA structure with B-DNA backbone conformation, for example, one uses the BDNA_X.pdb set to replace Atomic_X.pdb. There is a sub-command cp_std of the Ruby utility program x3dna_utils to help with this: x3dna_utils cp_std BDNA. This will copy BDNA_X.pdb to the current working directory and rename it Atomic_X.pdb. Please note that rebuild searches for Atomic_X.pdb files first in the current working directory, and then in $X3DNA/config.

To make the above description clear, here is an example. Go to the directory $X3DNA/examples/analyze_rebuild, and try to reproduce the following:

• use the command, x3dna_utils cp_std BDNA, so that you will have Atomic_X.pdb files
• use find_pair bdl084.pdb | analyze, to analyze the structure bdl084 (355d) and to generate a file named bp_step.par
• use rebuild -atomic bp_step.par bdl084_3dna.pdb, to generate the PDB file bdl084_3dna.pdb with a standard B-backbone

The RMSD between all atoms of the original bdl084.pdb file and the generated bdl084_3dna.pdb file is only 0.73 Å. Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken). This structure, however, serves well as a starting point for further energy minimization. See post "Restraint optimization of DNA backbone geometry using PHENIX" for how to regularize the overlong bonds.

[ry54451]

In this process, you generate the parameter file with two header lines.
I understand what the 1st line means.
What does the value associated with the 2nd line mean? I see that it is '0' , but why have it? What does it signify?

Thank you.

[xiangjun]

There are actually three header lines, as below:

Code: Bash

1.   12 # base-pairs
2.    0 # ***local base-pair & step parameters***
3. #        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     Shift     Slide     Rise      Tilt      Roll      Twist

The '0' in the second line means this parameter file is using local base-pair and step parameters, as detailed in the third line. This file is named 'bp_step.par' from the output of the 3DNA analyze program.

A parallel output file from the 3DNA analyze program, named 'bp_helical.par', has the following header lines:

Code: Bash

1.   12 # base-pairs
2.    1 # ***local base-pair & helical parameters***
3. #        Shear    Stretch   Stagger   Buckle   Prop-Tw   Opening     X-disp    Y-disp    h-Rise    Incl.     Tip     h-Twist

Hopy this clarifies the matter.

Xiang-Jun

[Shreya Ghosh]

I generated a proper .par file but I was not able to generate a proper pdb file. My pdb file only contains the DNA bases without the P, C5', C4' and other backbone atoms.

How can I amend the error?

Thank you.

[xiangjun]

Please provide details. Reproducibility is the key.

Xiang-Jun