Topics

1

MD simulations / auxiliary.par and analysis pdb files with multiple frames?

« 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.

2

General discussions (Q&As) / cannot execute binary file

« on: October 03, 2014, 01:02:28 am »

After I follow the installment procedure, including setting the environmental variables and home path, I type find_pair -h, I see something like:
-bash: /home/wwang02/x3dna-v2.1/bin/find_pair: cannot execute binary file

Although I use unix a lot, but still lack a basic understanding of the system. I wonder what it is wrong and what are the possible sources of problems?

Thank you

3

MD simulations / How is the helix axis calculated in 3DNA

« on: September 26, 2014, 10:12:09 am »

How does 3DNA define a helix? If I want to calculate a helix axis of a DNA, what position should I start to extend the local vector? and how should I calculate the base coordinates, by averaging all the atom coordinates of base pairs?

I need to know this, because I want to implement the analysis method of 3DNA to my simulations which are not done by the all-atom fashion. Does anyone know whether there exists any publications where I can refer to?

Thank you