Re: [AMBER] Generating LJ paramters of divalent copper ions

From: David A Case <>
Date: Sun, 3 Jan 2021 09:09:27 -0500

On Sat, Jan 02, 2021, angad sharma wrote:

Note that the ion parameters you want depend on the water model you choose.
We almost always use the cSPCE water model for RISM, so the ion parameters
to try first are this in leaprc.water.spce:

loadAmberParams frcmod.ionsjc_spce
loadAmberParams frcmod.ions234lm_126_spce

The first line is for monovalent ions, the second for divalents and higher.

For this set the Cu2+ parameters are:

Cu2+ 1.223 0.00160860

This doesn't mean that these are automatically the best values, since
divalents are hard to model, in either explicit or implicit force fields,
but this should be a good start.

There are many pairs of rmin/epsilon parameters that give similar results,
which is why the values in the MG.mdl file look different that those in the
corresponding frcmod file. I think the MG.mdl values have been optimized to
provide easier convergence in RISM.

In biochemical systems (where Amber is most commonly used) the free Cu2+
concentration is generally *very* low. If you are planning to work at
higher concentrations, you may need to run tests to make sure that you are
not getting too much ion pairing between Cu2+ and an anion like Cl-.

The file format and units are discussed in Section 7.8.1 of the Amber 2020
Reference Manual.

....good luck....dac

AMBER mailing list
Received on Sun Jan 03 2021 - 06:30:02 PST
Custom Search