Zmatrix
The webpage is to convert XYZ-file to USPEX MOL_1 file.
USPEX allows the prediction of crystal structure from the "ready-made" molecular unit.
If the structure can be described by the packing of some molecular motifs, this can save a lot of time.
The orginal methodolgy is described in
Zhu Q., Oganov A.R., Glass C.W., Stokes H.T. (2012) Acta Cryst. B68, 215-226.
And some nice applications can be found in
Zhou X.-F., Oganov A.R., Qian G.R., Zhu Q. (2012). Phys. Rev. Lett. 109, 245503.
To use this feature, one needs to prepare some additionl files (called MOL_1, MOL_2, etc.), which describe the structure of a molecule.
The constuction of these files is straightfoward.
Here we propose an online tool to assist this. One can simply prepare it in the following ways:
(1) Find the structural file (*.cif, *.pdb, .etc) from available database, remove the rest atoms,
make sure all the existing atoms are covalently bonded to other atoms, and export the structure in xyz format.
(2) Copy the xyz file to the text frame below, and click "convert" button.
(3) The program will automatically sort the atoms according to calculated topological relations.
In the right panel, you will see two output files. Zmatrix information tells information in terms of Zmatrix style (bond length, bond angle, torsion angle).
This can be very useful for checking the correctness of input. If it is reasonable, you can directly copy the results from USPEX MOL_* for your USPEX calculation.
(4) If you study flexible molecules, you need to modify the last column manually, indicating flexible angles.
If you meet any problem, please send the input xyz to Qiang Zhu.
Examples:
- example1: benzene (a general case used in USPEX)
- example2: aspirin for GULP (with charge and chemical labels)
Authors:
Qiang Zhu (main code),
Maksim Rakitin (web interface)