Rebuild with backbone from single-stranded .par file

[nicalleb]

Dear,

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