[QE-users] atomic positions/coordinates for single molecule

[Tone Kokalj]

Dear Tarek

A very elegant way to get molecular coordinates is via SMILES (symbolic
molecular specs) and OpenBabel.

SMILES: 
https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

OpenBabel: converts SMILES string to 3D coordinates
http://openbabel.org/ (on Debian-based linux distros, it can be
installed as: sudo apt install openbabel)

Here is the example for benzene molecule:

obabel -:"c1ccccc1" -oxyz --gen3D --best

This gives:

12

C          1.38312       -0.22147        0.00519
C          0.50712       -1.30686       -0.00780
C         -0.87101       -1.09040       -0.01489
C         -1.37270        0.21103       -0.00492
C         -0.49653        1.29628        0.01015
C          0.88132        1.07997        0.01382
H          2.45669       -0.39003        0.00977
H          0.89781       -2.32074       -0.01321
H         -1.55369       -1.93589       -0.02756
H         -2.44648        0.37945       -0.00872
H         -0.88753        2.31018        0.01944
H          1.56402        1.92535        0.02299
1 molecule converted

One can find SMILES online for very many molecules 
(e.g. on PubChem, https://pubchem.ncbi.nlm.nih.gov/)

Best regards,
Tone
-- 
Jožef Stefan Institute, Ljubljana, Slovenia


On Mon, 2024-02-19 at 22:11 +0200, Tarek Hammad wrote:
> Dear all
> 
> How can I obtain the atomic coordinates for single molecules??? for 
> solid state, It is well known for me.
> 
> Thanks a lot in advance.
> 
> Tarek Hammad.
> 
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