do_x3dna as a plugin for VMD and update in dnaMD

[Rajendra Kumar]

Hello,

I have developed do_x3dna as a plugin for VMD (http://do-x3dna.readthedocs.io/en/latest/vmd_plugin.html). Now, two variants of do_x3dna are available, one for GROMACS and other as a plugin for VMD.

Now dnaMD can be used as both Python module (http://do-x3dna.readthedocs.io/en/latest/api_summary.html)) and command line tools (http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html). I am still expanding the dnaMD command. dnaMD can be installed easily through pip (http://do-x3dna.readthedocs.io/en/latest/install_dnaMD.html).

With best regards,
Rajendra

[xiangjun]

Hi Rajendra,

Nice effort! Now do_x3dna and 3DNA are reaily accessible to the huge VMD user community.

Thanks for keep us informed of your new progress!

Xiang-Jun

[Beñat Olave]

Dear Rajendra,

We are a group from Spain, our research is focused in creating different functional DNA nanostructures.

We have just started using computational chemistry and after doing some MD simulations I wanted to study the trajectories of a dsDNA using your tool, I think it can provide very useful information.

Unfortunately, I had issues while installing its plugin for VMD in windows 10 (x86). Even if it seems it is correctly installed:
"package require do_x3dna
1.0"
When I execute any command "do_x3dna WHATEVER", it closes immediately.

I have just solved the closure deleting all the "exit" words from the script but it still gives me this error:

=================== ERROR ======================
 $X3DNA environment variable is not available.
 See below for usage.                           
================================================

I don't understand why, because I have already installed X3DNA correctly, I have used it for other analysis of a single step.

Could you help me?

Best regards,
Beñat Olave

[xiangjun]

Dear Beñat,

As a follow-up, I sent Rajendra an email message on May 2, asking him if he is still in support of do_x3dna. As with your questions here, I've so far not heard back from Rajendra. Based on my previous experience, I know he is very responsive. So, he may no longer support do_x3dna.

Best regards,

Xiang-Jun