AMBER Archive (2006)

Subject: Re: AMBER: divalent ions

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Tue Mar 14 2006 - 16:10:19 CST

> I presently have Amber 7 and I was wondering if Amber8 has divalent ions
> included in its ions library. If not, is there a way to add such ions to the
> library/force field?

There are a number of ways to find this information; for example, on the
AMBER WWW page at http://amber.scripps.edu you can type "divalent" or Mg2+
into the Google search bar to search the archives or the WWW page and a
number of hits come up that provide information...

Tutorial 4 from the AMBER Workshop linked at the AMBER WWW page shows how
to build a residue for Cu+; follow this procedure to develop a divalent
ion.

Alternatively, you can look through the $AMBERHOME/dat files to search
through the parameter files (dat/leap/parm/). Looking at parm94.dat
(Cornell et al. force field) I find C0 for calcium and MG for magnesium.
To find corresponding residue topologies, look either at the prep files
(dat/leap/prep/) or the lib files (dat/leap/lib/). In the leaprc.ff94,
reference is made to ions94.lib which defines MG2 (Mg2+). You could
define Ca2+ creating a new unit in LEaP (like in tutorial 4), by copying a
prep entry for an ion and altering the names (and charge) and then loading
it into LEaP with loadamberprep, or by directly editing the ions94.lib
file to add a new ion (or morph MG2 to CA2).

To find the actual parameters to use, I would search the literature for
work involving divalent ions. I note that the K/Cl/Mg2+ are not very well
balanced in Cornell et al. (parm94) such that you can get KCL salt
formation which is undesirable. I have used the standard Cornell et al.,
the Roux divalent ion parameters in CHARMM, and others in various
applications. The Beveridge group has a set of K/Cl/Mg2+ parameters used
in their DNA work, and there are likely others available, including
non-additive potentials for ions... (Potential authors to search may
include: Pettitt, P Smith, Roux, Dang, Caldwell, Merz, MacKerell, C. Lim,
Sponer, Auffinger, ...)

A PubMed search for ("molecular dynamics" divalent) pulls up ~50
references, ~half are simulation studies with divalent ions...

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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