DNA Helical Parameters Analysis

Every DNA helical parameter, backbone torsion, stiffness and correlation from an MD trajectory, with Curves+ and Canal.

by Temple Compute

Run DNA Helical Parameters Analysis on Horus

W-17 · DNA Helical Parameters

Every DNA helical parameter, backbone torsion, stiffness and correlation from an MD trajectory, with Curves+ and Canal.

Domain: BioExcel Building Blocks

Overview

Analyzes a DNA MD trajectory with biobb_dna (Curves+ and Canal). The example is the Drew-Dickerson dodecamer (CGCGAATTCGCG, PDB 1BNA), a 500 ns trajectory from BigNASim. Curves+ extracts helical parameters, Canal builds time series and histograms, and a fan-out of tasks computes averages, time series, stiffness, bimodality and correlations. The workflow has 70 tasks.

Pipeline

curves                  Helical parameters (Curves+)
canal                   Time series and histograms (Canal)
avg_*                   20 average helical parameters (step, base pair, axis, groove)
puckering, canonicalag, bipopulations   Sugar pucker, canonical alpha/gamma, BI/BII populations
ts_*                    36 time series of helical parameters and backbone torsions
average_stiffness, basepair_stiffness   Stiffness / elastic constants
dna_bimodality          Twist bimodality at the selected step
intraseqcorr, interseqcorr, intrahpcorr, interhpcorr, intrabpcorr, interbpcorr   Correlations

Inputs / Outputs

Inputs: solvent-stripped trajectory traj and matching topology top (defaults in TRAJ/), one double-stranded DNA with strand 2 numbered right after strand 1.
Outputs (results/): curves.out.lis, curves.out.cda, canal.out.zip, <param>.averages.{csv,jpg}, <param>.timeseries.zip, the selected-position series timeseries/series_<param>_step.csv (step parameters) and timeseries/series_<param>_bp.csv (base-pair parameters), twist.stiffness.csv, stiffness_bps.csv, twist.bimodality.csv, and the correlation CSVs (twist.intrabp_correlation.csv, twist.interbp_correlation.csv, helpar_bp(s)_correlation.csv, bp(s)_correlation.csv).

Parameters

| id | Default | Meaning | |---|---|---| | traj | TRAJ/structure.stripped.nc | NetCDF trajectory (500 ns dodecamer, BigNASim NAFlex_DDD_II) | | top | TRAJ/structure.stripped.top | AMBER topology matching the trajectory | | sequence | CGCGAATTCGCG | Strand 1, 5' to 3'; sets the Curves+ strand ranges and labels | | bp_step | 3 | Position read by the stiffness, bimodality and helical-parameter correlation tasks: step i (bases i, i+1) and base pair i. Valid from 2 to sequence length minus 2; the default is the C3G4 CpG step |