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MD simulations / Analysis of helical parameter of DNA with unnatural

« on: February 18, 2019, 06:09:48 am »

We are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, the base pair  DX:DY was not be recognized when I used “find_pair”. Notably, the unrecognized base-pair ( DX, DY ) are not typical purine or pyrimidine. How can I analysis the confirmation parameters with 3DNA in such case? 

  The PDB files of DX, DY,  and a frame of MD simulations(XY.pdb) are given in the attachment. Thank you very much!

Thanks and Best wishes

Priyabrata Das