Analysis of trajectory from Molecular Dynamics

[shvelarde]

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Given that do_x3dna seems to be outdated, I was wondering if still DSSR can not handle entire trajectories from MDs.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

[xiangjun]

Hi S h.v,

Thanks for using 3DNA/DSSR, and for posting your questions on the Forum.

Given that do_x3dna seems to be outdated, I was wondering if still DSSR can not handle entire trajectories from MDs.

Yes, try DSSR with options --md (alias --nmr) and --json.

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...

DSSR starts from standard PDB or mmCIF format, not any non-standard binary format.

Which web version of DSSR are you referring to? Please be specific.

Xiang-Jun

[shvelarde]

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

[xiangjun]

Hi Salvador h.v,

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?

The http://wdssr.x3dna.org website was developed by Dr. Shuxiang Li, a former postdoc from the Olson lab at Rutgers. Shuxiang has left a while ago for another position. He may chime in to answer your questions, but I am not sure.

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.
...

Please attach your nuclei_50Frames.pdb file together with the specific commands and messages. Reproducibility is the KEY.

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.

In this case, you may want to first become familiar with well-documented cases in whatever packages you are using. I am not a practitioner of MD simulations, and I cannot provide advices in that filed. If you want to pursue DSSR further, I'd be happy to guide you through any technical aspects.

Xiang-Jun