Repository navigation
Very new user: Calculate the cartesian atomic coordinates for a molecule #188
Description
All,
I would like to calculate for a given molecule the cartesian atomic coordinates in Angstroms. Would it be possible to have a working example to do this that would allow me to vary the input molecule and get as an output, ideally in a simple text file, the above?
I would very much appreciate any help here, I am new to the code. I appreciate I will need to understand eventually aspects relating to optimisation options and the model used PM3/PM7. But a working example with trusted defaults would be most welcome.
Many thanks,
Activity
nbehrnd commentedon Jan 11, 2024
What is the file format your molecule of interest is described? Because there are a couple of them, the most elementary the .xyz, where atoms' positions are described in a Cartesian coordinate system with (an implicit) scale in Angstrom. See e.g., openbabel.
If "calculate for a given molecule the cartesian atomic coordinates" refers to a conversion of the underlying file format, openbabel (with its optional gui) might suffice. Examples of conversion are compiled here.
If you seek a GUI to set up a subsequent computation for instance with MOPAC, avogadro and its input generators is one example of a helpful assistant: