Hi Rajib,
Probably part of the confusion is due to the meaning of "determine the
structure". I understand "determine" can have different meaning in
different contexts. In my area of research "determine" generally means to
use experimental methods like X-ray crystallography or NMR to establish the
structure of a molecule.
What PyMOL does is to "guess" the topology of a molecule based on some
"chemical rules", distance cutoff and information in files (like Cartesian
coordinate of atoms in PDB files). There is no QM method involved in any
part of the procedure not even semi-empirical or classical force-fields.
If you want to study chemical reaction, theoretically, you need to use QM
methods, and PyMOL is not the software for that.
Please feel free to send me a private message if you want further details
on this topic.
Best,
Osvaldo.
On Thu, Jun 1, 2017 at 9:26 PM, Susmita/Rajib <bkpsusmi...@gmail.com> wrote:
> No, Dr. Wassenaar, Sir! People have confused me. After two years, I am
> told that:
> [Quote]PyMol does not use QM methods. It also does not "determine the
> structures of molecules" [/Quote]
> I need my illustrious peers to clarify me regarding all my queries in
> all my posts in the present thread.
>
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