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Questions and answers => MD simulations => Topic started by: Rajendra Kumar on November 01, 2017, 06:16:55 am

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Title: do_x3dna as a plugin for VMD and update in dnaMD
Post by: Rajendra Kumar on November 01, 2017, 06:16:55 am
Hello,

I have developed do_x3dna as a plugin for VMD (http://do-x3dna.readthedocs.io/en/latest/vmd_plugin.html (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 (http://do-x3dna.readthedocs.io/en/latest/api_summary.html))) and command line tools (http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html (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 (http://do-x3dna.readthedocs.io/en/latest/install_dnaMD.html)).

With best regards,
Rajendra
Title: Re: do_x3dna as a plugin for VMD and update in dnaMD
Post by: xiangjun on November 01, 2017, 08:29:13 am
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
Title: Re: do_x3dna as a plugin for VMD and update in dnaMD
Post by: Beñat Olave on April 30, 2019, 12:33:50 pm
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
Title: Re: do_x3dna as a plugin for VMD and update in dnaMD
Post by: xiangjun on May 27, 2019, 12:16:26 pm
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

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.