On Thu, Oct 07, 2021, Małgorzata Kogut wrote:
>
>I would like to kindly ask you if there available parameters for the
>following ions: cadmium(II), mercury(II), lead(II) and copper(II) in order
>to run MD simulations in Amber?
Yes: you get them automatically when you source leaprc.water.xxx, where
"xxx" is your chosen water model. The source is in
$AMBERHOME/dat/leap/lib/atomic_ions.lib, where you can see the residue and
atom names you need to use (chosen by the PDB, not by us.)
There is also a nifty new Web page (thanks Maria and team!) about this:
https://ambermd.org/AmberModels_ions.php
....dac
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Received on Thu Oct 07 2021 - 05:00:02 PDT
