Messages

1

MD simulations / Re: x3dna_ensemble extract output naming

« on: December 05, 2015, 05:39:39 pm »

Dear Xiang-Jun,

Thank you for the speedy reply. I have tried single PDB with "analyze", the output .outs file is much easier to understand with all the labels and annotations.  But I haven't tried x3dna_ensemble with single PDB. I'll try that and see if I can understand better. Nice weekend.

Wai

2

MD simulations / x3dna_ensemble extract output naming

« on: December 05, 2015, 11:40:50 am »

Dear Dr. Lu,

I am new to 3DNA. I am trying to analyze a MD trajectory created by GROMACS of its base-stacking properties. I have used find_pair to get the base-pair parameters file, then used x3dna_ensemble analyze to produce an output file without much problem. However, after I used x3dna_ensemble extract -a, I got a number of .out files of which I do not know how to use. I assume the files with *_area.out and *_area0.out are the relevant files reporting base-stacking overlap areas, are these not? Which one should I look at? My structure is a single-stranded stem-loop. The stem is picked up by find_pair correctly. And also, what are the various columns in these two .out files?

A second question is if I can do similar thing to "find_pair -s RNA.pdb | analyze" to my MD ensemble using x3dna_ensemble? I hope to be able to do this to look at stacking areas in the non-paired bases in the loop and see their changes over MD time.

Thank you very much for your reply. I am sorry I tried to look at various places including this forum, the 2 papers but could not find the answer.

Wai