Hi Aashish,
Just a thought, which is not an accurate way to solve the problem.
In the UFF paper: https://pubs.acs.org/doi/10.1021/ja00051a040 <https://pubs.acs.org/doi/10.1021/ja00051a040>, there are VDW parameters about Au+++ ion, which is the "Au4+3” atom type. These parameters may not be suitable to use for the atomic ions in solutions.
You can check these two webpages: http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm> and http://ambermd.org/tutorials/advanced/tutorial20/12_6.htm <http://ambermd.org/tutorials/advanced/tutorial20/12_6.htm> about how to model ions with the 12-6 model.
Pengfei
> On Jul 17, 2018, at 7:18 AM, Aashish Bhatt <aashish.ph16221.inst.ac.in> wrote:
>
> Dear amber members
>
> I have a peptide system and I want to solvate the peptide with water and
> Au+++ ion.
> I have looked at the AMBER ion library but Au parameter is not available.
>
>
> Can you suggest or guide me for preparation of Au ion parameter?
>
> Regards
> Aashish Bhatt
> INST-Mohali
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Received on Sat Sep 08 2018 - 12:30:04 PDT
