3DNA Forum

Questions and answers => MD simulations => Topic started by: drknnetz on August 12, 2015, 05:23:29 pm

Title: A-Form B-Form RNA/DNA
Post by: drknnetz on August 12, 2015, 05:23:29 pm: Does anyone know where to find the specifics as to how x3dna paramaterizes whether the RNA is in A form and the DNA is in B form? What coordinates does it use in the DNA molecule or RNA molecule?
Title: Re: A-Form B-Form RNA/DNA
Post by: xiangjun on August 12, 2015, 06:12:39 pm: It is not clear to me what you mean. Basically, 3DNA uses the so-called Zp parameter to decide if a DNA duplex is in A- or B-form. RNA duplex is nearly always in A-form. Please see the 2003 3DNA Nucleic Acids Research paper, and the A-form conformational motifs in ligand-bound DNA structures (http://www.ncbi.nlm.nih.gov/pubmed/10891271) paper for details.

HTH,

Xiang-Jun
Title: Re: A-Form B-Form RNA/DNA
Post by: drknnetz on August 12, 2015, 07:25:42 pm: I was basically trying to determine what parameters were used when the software determines A form or B form so I could validate the results from the program to my MD simulations. I will read the paper, thanks for the reference. You are very prompt and helpful!
Title: Re: A-Form B-Form RNA/DNA
Post by: metoo on March 23, 2017, 07:53:55 am: Dear All

Where exactly is the output for Zp written? I was unable to find a user manual or specific documentation.

Thank you !
Title: Re: A-Form B-Form RNA/DNA
Post by: xiangjun on March 23, 2017, 10:44:59 am: Using 355d as an example,

Code: [Select]
find_pair 355d.pdb | analyze

Check the output file 355d.out, which contains a dedicated section that includes Zp values used in the 2000 JMB paper.

Xiang-Jun