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1. I notice there are a bunch of data about DNA helixes in auxiliary.par. Does anyone know where I can find documents explaining what they are in detail, so that I can decide which is important to me.The auxiliary.par is meant to be auxiliary, and the meaning of each section should make more sense after you read x3dna_v1.5.pdf and tech_details.pdf distributed with 3DNA (in the $X3DNA/doc folder). If you have specific questions about a particular section, please post them here.
2. Does anyone know how to analyze pdb files that contains multiple frames? I notice when 3DNA analyze those files, it only produce output for the first frame.You can try the Ruby script x3dna_ensemble in 3DNA v2.1. If you are performing analysis of DNA/RNA dynamics in MD simulations, you may find Rajendra Kumar's do_x3dna (http://rjdkmr.github.io/do_x3dna/) useful.
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.