Messages

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) / Re: cannot execute binary file

« on: October 03, 2014, 10:51:24 am »

Here is the output I got.
uname -a:
Linux greentail.wesleyan.edu 2.6.18-194.el5 #1 SMP Tue Mar 16 21:52:39 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux

ls -l $X3DNA/bin/find_pair:
-rwxr-xr-x 1 wwang02 s16 437552 Jul  9 11:33 /home/wwang02/x3dna-v2.1/bin/find_pair

Thank you

3

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

4

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

« on: September 29, 2014, 11:33:18 pm »

Thank you for replies!

5

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

« on: September 26, 2014, 03:38:53 pm »

If the DNA simulation is done in a coarse grain fashion, can I calculate the center of mass of triads and build up local unit vectors, and average the all the unit vectors to define the helix axis? Do you think that would be close enough to the method you use in the paper?

6

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