3DNA Forum

Questions and answers => MD simulations => Topic started by: souviksur on February 25, 2012, 01:46:59 pm

Title: Interpretation of Analysis data from 3DNA
Post by: souviksur on February 25, 2012, 01:46:59 pm: Hello Everybody,

I have done some analysis in 3DNA, and got output files from it.
But cannot able to interpret it, can you please guide me for that, I am attaching output files,
And I also want backbone parameters to generate from 3DNA, how can I do this?
I shall be so grateful if you please suggest any reference paper regarding it.
Please do reply.
Title: Re: Interpretation of Analysis data from 3DNA
Post by: xiangjun on February 25, 2012, 01:51:59 pm: What you attached are just input files generated from find_pair. Please provide .pdb files and output files to illustrate more clearly the problems you have, then others may help you more concretely.

Xiang-Jun
Title: Re: Interpretation of Analysis data from 3DNA
Post by: mauricio esguerra on February 25, 2012, 02:06:09 pm: Hi,

It seems like you have only run find_pair.
You now have to run analyze to get the output file with rigid-body parameters and more.

Code: [Select]
analyze normal_10ns.inp analyze modified.inp
This will produce the output files normal_10ns.out and modified.out.

I suggest looking at the documentation (e.g. x3dna_v1.5.pdf) which you can find in the doc folder.
Title: Re: Interpretation of Analysis data from 3DNA
Post by: souviksur on February 27, 2012, 08:53:09 am: hello

please find the pdb file related to the .inp file, I have also "analyze" it and got some data but those data did not contain any backbone angle parameters.
Title: Re: Interpretation of Analysis data from 3DNA
Post by: xiangjun on February 27, 2012, 05:38:36 pm: Your two attached PDB files helped me trace and fix the bug -- it was the non-DNA/RNA chain that caused the problem. The bug can be traced way back to SCHNAaP, on which analyze in 3DNA is based. I've updated v2.1beta in the download page. Please have a try and report back how it goes.

For reference, I have also attached the output files that correspond to the two PDB files.

Xiang-Jun
Title: Re: Interpretation of Analysis data from 3DNA
Post by: souviksur on February 29, 2012, 02:05:47 am: Please send me the link to download 3DNAv2beta version.

thanks
Title: Re: Interpretation of Analysis data from 3DNA
Post by: mauricio esguerra on February 29, 2012, 02:52:11 am: http://forum.x3dna.org/downloads/3dna-download/