I would like to simulate a crystal structure in Gromacs, but all I have are XRD results in txt format. Is there any way that I could convert it to a .pdb or .gro file? I know someone has asked a similar question and was pointed to openbabels. But I have read the tutorial of openbabels and didn't find xrd file supported.
To run simulations in Gromacs, you need structure (gro or pdb file) and (!) topology (top file). While the former may be a matter of few lines in awk or python, you may face some problems when generating the top file.
What kind of structure is it? Biomolecule? Periodic small molecule(s)? A solid-state structure? Are there chemical bonds crossing the periodic boundary?
Hey Michal,
Thank you so much for answering.
It's a metal hydroxide structure, which I will use as a non-moving part in a organic-inorganic hybrid system. There will be no bonds crossing the periodic boundary.
Thanks!
Sounds it should not be so difficult...
I'm not aware of any available tool to convert the files automatically, but as the xrd is a text file, the basic knowledge of input/ouput methods of awk, python, ruby etc. should be sufficient to generate both gro and top files. Unfortunately, I can't provide any further details... Good luck.
- Badges
- Science method
- Similar topics
- Methodology
- Crystallography
- X-ray Diffraction
- XRD Analysis