On Wed, Jan 08, 2014, Mahendra B Thapa wrote:
>
> Naturally, I can see how Ca-atoms are connected with ligands on that
> original pdb using Chimera or VMD.
You have to think carefully about the meaning of the word "connected". There
are "close contacts", i.e. short distances between Ca and various oxygen
atoms. These won't be changed by tleap, and you can examine them using the
usual distance commands in Chimera, VMD or cpptraj.
Unless you explicitly add them, there will be no "bonds" (in the molecular
mechanics sense) between Ca and the oxygens. In general, metal ion--ligand
interactions can be modeled either with or without molecular mechanics bonds.
But if you want the option with bonds, you have to add them yourself, and add
the parameters needed as well.
...hope this helps...dac
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Received on Thu Jan 09 2014 - 05:00:02 PST
