AMBER Archive (2009)

Subject: Re: [AMBER] What is the default position of the partial charges?

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Wed Mar 04 2009 - 15:44:20 CST

> What is the default position of the partial charges?
>
> Is it in the center of the atom?

Yes.

> Can I change the position of the partial charges for each atoms?
>
> How do i change the position of the partial charge in an easy way?

You cannot. The easiest way to do this in the current code is to consider
"extra points". These are special beasts that have a charge, no van der
Waals and are somehow constrained to their parent atom. The "somehow
constrained" has its limits. The TIP4PEW water model uses this concept as
do some of the polarized force fields.

Alternatively you could implement Drude oscillators or use the dipole (and
higher order) terms in the polarization code and/or AMEOBA code.

In any case, it will be challenging to do correctly and require fairly
deep understanding of polarization, polarizable models, and AMBER (PME).

--tec3

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