Can anyone help me to run do_x3DNA (part of 3DNA tool) for GROMACS 5 trajectory files? I have installed it in a server, and run the command, and its showing segmentation error, so anyone who is having experience in 3DNA tool. Please help me.
Have you read http://rjdkmr.github.io/do_x3dna/usage.html ?
It seems there are specific considerations for version 5.0 (e.g., the .tpr file is compatible, so you need to use a PDB file).
Hi Dhanusha,
What you can do, if you like, is extract each frame of the trajectory as pdb and calculate them using x3DNA by a shell script. The script should be such that it will automatically but sequentially took the pdb file and give input to x3dna.
Not a good and brilliant idea but you can do this.
Regards
Aditya
Hi Dhanusha,
Presently, do_x3dna can be only compiled and installed using Gromacs 4.5/4.6 versions. Therefore, tpr file from 5.0 version is incompatible with do_x3dna. A PDB file can be used in place of tpr file with "-s" option. Also, only PBC corrected (molecule not broken) trajectory and PDB file should be used as inputs.
Regards,
Rajendra
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