On Mon, Aug 29, 2022, 幅田揚一 via AMBER wrote:
>
> I am a new user and beginner of Chimera and MD simulations. In our
>research group, I want to do MD simulations of complexes with Ag+ ions.
>By downloading Amber Tools, will we be able to use Amber's force field that
>allows us to use Ag+?
As Dr. Horn indicated, the answer is generally "yes". But it depends
somewhat on what the Ag+ ions are interacting with: can these interactions
be treated as non-bonding interactions? If so, things should be pretty
straightforward. If you need to generate force fields for covalent bonds
between silver and its ligands, that is more complicated. There are tools
to help you out, but be prepared for more setup work.
One thing to look out for is nomenclature, since silver has two common
oxidation states: The ion in the Amber library named "AG" is Ag+, whereas
the ion named "Ag" is Ag2+. There are no real standards in protein
crystallography (and hence in PDB files that we biochemists usually work
with.) Be aware that Amber is oriented towards macromolecules, not towards
inorganic chemistry.
...hope this helps....dac
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Received on Mon Aug 29 2022 - 13:30:04 PDT
