Messages

1

MD simulations / Re: do_x3dna as a plugin for VMD and update in dnaMD

« 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

2

General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild

« on: November 06, 2018, 07:15:06 pm »

Hello, I made it copying and renaming the files, I still have to elucidate how to use MSYS2, as soon as I do I will post it.

Best regards.

3

FAQs / Re: How to set up 3DNA on Windows

« on: November 06, 2018, 06:15:32 pm »

Hello, it says:

"
$ dir %X3DNA%config\version
The volume of unit C has no label.
The serial number of the volume is: A2CF-EF3C
Directory of C:\Users\Benat\x3dna-v2.3\config
05/11/2018  22:15                68 version
               1 file                68 bytes
               0 dirs  101.483.311.104 free bytes
"

4

General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild

« on: November 06, 2018, 02:19:36 pm »

Yes, sorry, it says:

"is not recognized as an internal or external command, operable program or batch file"

5

General discussions (Q&As) / Re: 3DNA 2.4.3 Rebuild

« on: November 06, 2018, 02:04:47 pm »

Hello, this is an example:

6

FAQs / Re: How to set up 3DNA on Windows

« on: November 06, 2018, 01:53:37 pm »

Hello, here is the image

7

General discussions (Q&As) / 3DNA 2.4.3 Rebuild

« on: November 06, 2018, 01:11:05 pm »

Hello,

I wanted to rebuild the DNA with backbone included but typing "cp_std" before adding rebuild command is not working, neither typing "x3dna_utils cp_std" as shown in help. They are not recognized as commands.

I would appreciate a possible solution 

8

FAQs / Re: How to set up 3DNA on Windows

« on: November 06, 2018, 01:06:47 pm »

Hello,

I did it in windows 10 and I think I put everything okay (I followed all the steps presented here with ConEmu):

The output is:
"C:\Users\Benat\x3dna-v2.3\"

I fixed it creating just another folder for config with the name of "x3dna-v2.3config"

I am just learning how to use the program, I have another issue that I will post in bug reports (but probably is my fault)

Edited: Maybe the .zip you tested is not the same as the uploaded one? And that's why there is something missing?

9

FAQs / Re: How to set up 3DNA on Windows

« on: November 06, 2018, 11:30:52 am »

Hello, I think there is an error with the update of today:

Benat@SURFACE-OLAVE C:\Users\Benat
$ find_pair -h
open_file <C:\Users\Benat\x3dna-v2.3config/version> failed: No such file or directory

Best regards and thanks for your effort.