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Questions and answers => MD simulations => Topic started by: wwang02 on October 05, 2014, 04:55:54 pm

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Title: auxiliary.par and analysis pdb files with multiple frames?
Post by: wwang02 on October 05, 2014, 04:55:54 pm

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.

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.

Title: Re: auxiliary.par and analysis pdb files with multiple frames?
Post by: xiangjun on October 06, 2014, 02:48:01 pm

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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.

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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.

HTH,

Xiang-Jun

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