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. > > _______________________________________________ > The Quantum ESPRESSO community stands by the Ukrainian > people and expresses its concerns about the devastating > effects that the Russian military offensive has on their > country and on the free and peaceful scientific, cultural, > and economic cooperation amongst peoples > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users _______________________________________________ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list [email protected] https://lists.quantum-espresso.org/mailman/listinfo/users
