Very new user: Calculate the cartesian atomic coordinates for a molecule
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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,
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:
