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Topics - nicalleb

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I would like to rebuild a stacked nucleobases structure from a .par file (with the 6  base-step parameters, see in attachment). This .par file was obtained by analyzing a single-stranded GTT stack (PDB file) with the command "find pair". If I rebuild my structure from this .par file with the following command :

rebuild -atomic bp_step.par test_rebuild.pdb

I get a structure without backbone and I need the backbone in subsequent calculations.

With the "Rebuilding" module of the online version of X3DNA, I know it is possible to have a structure with backbone, even starting with a .par file for a single-strand (containing only 6 local base-step parameters)

Is it also possible in command line (with the downloaded version of the software) and if so, how ?

Thank you in advance,

Nicolas Callebaut

General discussions (Q&As) / Local base step parameters
« on: July 13, 2020, 02:23:34 pm »
Hello everyone,

I study the ionization of small complexes composed of several stacked DNA bases. The values of ionization potentials seem to be very dependent of the conformational parameters. I use web-X3DNA to determine the local base step parameters (shift, slide, rise, tilt, roll and twist) of my complexes. I would understand how these parameters are determined by the software (because My results are very variable).

In that purpose, I looked for information in the tutorial and in some articles related to the program but it doesn't really help me. I've namely found that X3DNA adopts the standard reference frame for the parameters but again, it doesn't help me much. Do you have detailed information about the determination of the parameters by X3DNA or can you indicate me where I can found more precise information ?

Thank you in advance,

Nicolas (PhD student at ULB, Belgium)

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.