Web 3DNA Error

[Pierred]

Hi,

I'm a very new user. I'd like to use 3DNA as a tool to analyze RNA structures after they have undergone MD simulations.

As a quick test, I tried to analyze a pdb from my trajectory on the web interface Web 3DNA, but I get the following error: "Loading...Please wait. unable to open file pdbid.inps"

Do any of you know what I'm doing wrong? Is there anything I can modify in the pdb itself to make the analysis work?

Thank you for your help.

[xiangjun]

Hi,

Thanks for using 3DNA and for asking questions on the Forum. I've informed Rutgers on the w3DNA-specific issues, and hopefully the problem can be solved soon.

For the analysis of RNA structures, especially those from MD simulations, I'd strongly suggest that you try DSSR (http://docs.x3dna.org/dssr-manual.pdf). DSSR has options that faciltiate MD analyses. See my recent blogpost "DSSR is fast for MD analysis".

For your attached structure 805.pdb, running DSSR is as simple as: x3dna-dssr -i=805.pdb

From the DSSR-derived secondary structure in .ct notation, you can use VARNA to generate the attached figure.

HTH,

Xiang-Jun

[shuxiang]

The error you got is because our current web 3DNA version cann't recognize the A3 residue in your structure.  The web 3DNA  was developed 10 years ago and it uses an old version of 3DNA for analyzing DNA structures and the "A3" residue is not in the base list.  As Xiang-Jun suggested, you can use DSSR to analyze your structure. By the way, we're working on an updated version of web 3DNA.

[Pierred]

Perfect!

Thank you for your quick replies. It works really well with DSSR.

Replacing the "A3" residues to "A" also works on the web 3DNA interface.