Messages

1

RNA structures (DSSR) / Re: Analysis of trajectory from Molecular Dynamics

« on: July 08, 2020, 01:49:47 pm »

Hi Xiang-Jun,

Thanks a lot for your quick response.

I have a molecular dynamics (gromacs) trajectory: name.xtc. I upload this trajectory in vmd,  I removed the water and ions and saved
only 50 frames of the nucleic acids in a pdb format.

Then, I tried:

a) the webserver: http://wdssr.x3dna.org/analyze/. However, I am confused, the obtained results are for the 50 frames or only for the first one? I mean, the results are a statistical average?

b) dssr in the terminal using: x3dna-dssr -i=nuclei_50Frames.pdb --nmr
However I got the following message: no models found: ignoring the --nmr option.
Then, it shows
Processing file 'nucleci_50Frames.pdb',  and then show the results for presumably the first frame.

I suppose that I have an incorrect format in my pdb file. Because, the same command works fine with the included example  of x3dna (old 2.4version)
x3dna-dssr -i=sample_md0.pdb --nmr
However, the results are individual analysis of each frame, right? I mean, the results are not an statistical average?

To be sincere, is the first time that I perform MDs of DNA-B. I am just trying to figure out what physical quantities are more suited to
quantify the deformation of the DNA.

Thanks a lot

Salvador h.v

2

RNA structures (DSSR) / Analysis of trajectory from Molecular Dynamics

« on: July 07, 2020, 11:53:48 pm »

Dear Professor Xiang-Jun,

I found this old post (http://forum.x3dna.org/feature-requests/trajectory-over-time/) regarding the analysis of an entire trajectory from MDs.

In that post your response was: 3DNA -- you may want to try the x3dna_ensemble Ruby script...
                                                   using do_x3dna and 
                                                   DSSR -- there is no similar functionality yet

Given that do_x3dna seems to be outdated, I was wondering if still DSSR can not handle entire trajectories from MDs.

Also, I would like to ask, if I have a complete trajectory in some binary format and I convert such trajectory to a pdb file, DSSR would be able to
analyze the trajectory? The web version of DSSR seems to handle trajectories for around 50 frames...


Thanks a lot in advance

S h.v