Re: [AMBER] Counter Ions in X-Ray structure.

From: David Case <>
Date: Thu, 27 Sep 2018 20:29:38 +0000

On Thu, Sep 27, 2018, Matias Machado wrote:
> The only issue you have is choosing the proper parameter set, because
> (1) there are several option available at $AMBERHOME/dat/leap/parm
> and (2) MG is not a trivial ion, so their parameters may be different
> in solution or at a binding site and even more, with a simple 12-6 LJ
> potential is not possible to fit all its experimental properties at once
> (i.e coordination number and binding energy)..

It is certainly true that there are a variety of possible force fields for MG
ions, and that studying the literature is important.

Having said that, the Amber developers have placed into the
leaprc.water.xxxx files the parameters that we believe are the most useful
to the widest variety of users, and should serve as good starting points.

So, our starting recommendation is to upgrade to AmberTools18, and include
a "source leaprc.water.xxxx" command in your tleap script. You can examine
these leaprc.water files to see which frcmod files we chose.

(We are *not* making recommendations about which water model to choose,
only which ion parameters are most likely to be compatible with the water
model you choose.)

This is done in an attempt to strike a balance between simplicity (just choose
recommended values) and flexibility (experiment with various alternatives.)


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Received on Thu Sep 27 2018 - 14:00:03 PDT
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