3DNA Forum

Questions and answers => MD simulations => Topic started by: shengxiehuang on September 18, 2017, 09:31:20 am

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Title: How to analyze helical parameters of DNA with unnatural bases
Post by: shengxiehuang on September 18, 2017, 09:31:20 am

Dear Mr Lu,
  Recently, we are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, base pairs DX:DA / DY:DA / DZ:DA can’t be recoganized when I used “find_pair”. Notably, the unrecoganized base-pair (named DX, DY, DZ, DA) are not typical purine or pyrimidine. How can I analysis the conformation parameters with 3DNA in a such case. 
  The pdb files of DX, DY, DZ, DA and a frame of MD simulations are given in the attachment . Thank you very much!

Best wishes!

Xiehuang Sheng

Title: Re: How to analyze helical parameters of DNA with unnatural bases
Post by: xiangjun on September 18, 2017, 10:38:50 pm

Hi Xiehuang,

I've had a look of your attached PDB files. DX/DY/DZ deviate too much from normal purines in terms of base orientation and atoms nomenclature, as shown in the attached image for DX. They are no longer recognized as nucleotides so "find_pair" cannot identify any pairs associated with them. This is clearly a limitation of 3DNA.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.