How to build different sugar pucker model

[lvelve0901]

Hi, xiangjun,

How is everything going?

I have a question about how to build a model sugar with different sugar pucker? I am assuming there is an easy way to do that but I don't know.

I know that you can calculate v0-v4 based on equation:ν_i = τ_m*cos(P+144(i-2))
Every time when I adjust v0-v4 dihedral angle in pymol or Gaussian, those dihedral angle always change correlated (because they are linked), like if you vary v0, then v1, then v2, then v3, then v4, and after that you go back to v0, the v0 will change again. Besides, the sugar Carbon Carbon bond length will also vary in this procedure.

I guess I am just wandering is there any way to synthesize a sugar model yielding an exact phase angle and amplitude (also better control bond length) as what I want.

The reason why I want to build this model because I want to perform DFT chemical shift calculation on different sugar pucker. The annoying thing is DFT is sensitive to certain bond length or bond angle, that's why I want to do a good control of these detail.

Thank you so much.

Best,
Honglue

[xiangjun]

Hi Honglue,

Thanks for your question on building a sugar model with a specified pucker, and controlled bond lengths and valence angles. Unfortunately, 3DNA does not have this functionality, and I am not aware of any other tools (in addition to PyMOL and Gaussian) that can do exactly what you want. I sense you may have to write some code yourself.

Sorry I cannot be of more help on this matter.

Xiang-Jun