How to calculate/measure base stacking parameters for ssDNA?

30 January 2024 0 10K Report

Dear all,

I have done md simulation of ssDNA on gromacs. Now I would like to determine the base stacking parameters such as rolling, twisting, tilting of two adjacent bases.

However, all the software x3dna, NAFlex, BioBB, measure the parameters for dsDNA.

Does anyone know how I can do the measurements for ssDNA?

I shall be be grateful

Thank you

Ayesha

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