Stacking Strength for Individual Nucs (General Question)

lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings

https://dna.physics.ox.ac.uk/

GNU General Public License v3.0

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Stacking Strength for Individual Nucs (General Question) #54

Closed dhollis6 closed 1 year ago

dhollis6 commented 1 year ago

Hello again--

The sequence parameter file(s) allows us to change the bonding strengths between A, G, C and T. Is there a way to change bonding strengths for individual nucleotides? Let's say I don't want nucs 14 and 15 to stack with each other, but I still want them to hybridize to their complements and stack to their neighbors (13 and 16, respectively). Is this possible?

Kind regards Daniel

lorenzo-rovigatti commented 1 year ago

Hi! Nope, that's unfortunately not possible at the moment.

dhollis6 commented 1 year ago

Alright, thanks for the quick reply :)

Daniel