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General discussions (Q&As) / Calculate torsion angles of the DNA, without taking into account the bases
« on: September 10, 2022, 06:48:52 pm »
Dear Dr. Xiang-Jun Lu,
I used versions of 3DNA earlier than the 2018 versions some time ago, in those versions it was possible to calculate the torsion angles of the sugar-phosphate backbone of DNA, without taking into account the bases, with the following command:
analyze -t = name.tor name.pdb
However in the new versions, this task is not possible anymore, it is necessary to have the nitrogenous bases or at least N1, C2 or N9, C4 atoms.
I was wondering if there is a new instruction or way to do that, because it would shorten my work route considerably. One of my study purposes is the optimized fragments of the Sugar-Phosphate Backbone, in these fragments the nitrogenous bases of the DNA are eliminated and replaced by a hydrogen (position N1 or N9) as shown in file attached .
Thank you very much,
Andrea R.
I used versions of 3DNA earlier than the 2018 versions some time ago, in those versions it was possible to calculate the torsion angles of the sugar-phosphate backbone of DNA, without taking into account the bases, with the following command:
analyze -t = name.tor name.pdb
However in the new versions, this task is not possible anymore, it is necessary to have the nitrogenous bases or at least N1, C2 or N9, C4 atoms.
I was wondering if there is a new instruction or way to do that, because it would shorten my work route considerably. One of my study purposes is the optimized fragments of the Sugar-Phosphate Backbone, in these fragments the nitrogenous bases of the DNA are eliminated and replaced by a hydrogen (position N1 or N9) as shown in file attached .
Thank you very much,
Andrea R.