rjdkmr / do_x3dna Goto Github PK

Hello,

I am recently performing elastic modulus analysis for my DNA structure. As I perform saveAsH5, I got this error:

FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = 'dna.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Note that I already performed elastic modulus analysis on other DNA structures. Weirdly, this error occurred in the first place.

I hope someone can help me regarding this matter. Thank you.

Dear Mr. Kumar.

Thank you for creating the tool.

I have gromacs 2023 on my machine. I am trying to compile the do_x3dna. it gives me this error
...............................
In file included from /home/ayesha/do_x3dna/src/do_x3dna.cpp:46:
/home/ayesha/gromacs-2023/src/gromacs/commandline/filenm.h:48:10: fatal error: gromacs/fileio/filetypes.h: No such file or directory
48 | #include "gromacs/fileio/filetypes.h"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [src/CMakeFiles/do_x3dna.dir/build.make:76: src/CMakeFiles/do_x3dna.dir/do_x3dna.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:98: src/CMakeFiles/do_x3dna.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
......................................................................................

I checked the paths of the mentioned files' they appear correct and the files are also there in the folders.

How can i remove the error?

Thank you

Best

Ayesha Fatima

Turkey

Dear Rajendra
Thanks for the very interesting utility.
Good news. Build with Gromacs-2019 (4 )/ Windows10 VisualStudio2019 successfully passed and works. But I had to fix some portability issues and errors - if the xtc file contains only DNA/RNA (solvent and ions excluded), the function reset_x causes exception because out of range on the array. In addition, I had to put additional protection - sometimes there are system races ?/caching? when opening/closing a file with find_pairs.
If this is interesting, I attach a patch for further development of the project.
I will test on versions of gromacs 2020 and 2021.
RAMDisk required.
Best regards, Boris.
diff.txt

Could you please suggest how can I install and use this tool with trajectory files generated using Gromacs 2021.1 version?

Hello, Mr Kumar. I want to use the file "BackBoneCHiDihedrals_g.dat" to plot Conformational wheel using backbone torsion angles. I use python scripts of the tutorial(https://do_x3dna.readthedocs.io/en/latest/notebooks/backbone_torsion_wheel_tutorial.html) to plot. But I can't plot
Backbone torsional angles wheel.
so I want to ask you how to plot Backbone torsional angles wheel. Woud you please provide me the out data file backbone_torsion_wheel_tutorial. Thank you very much!