AMBER Archive (2008)

Subject: AMBER: RE: Force Field Parameterizing

From: FyD (
Date: Tue Mar 25 2008 - 14:42:03 CDT

> On Mon, Mar 24, 2008, Shultz, Jack wrote:
> I'm looking at the H-Cluster for Fe-Hydrogenase, trying to generate a
> topology file. Xleap does not have bond parameters for Iron. So I tried to
> generate the parameters using antechamber and got these error messages. In
> order to find parameters should I harvest from literature or is there
> another way to generate the parameters I'm seeking.
> I understand these transition metals present theoretical problems with their
> complicated orbitals. Is Amber well suited for this type of problem?

You can convert a PDB file into a Tripos mol2 file and load the latter
in LEaP. By this way, you will create a correct topology for your
molecule (or your molecule fragment). This Tripos mol2 file might
contain atomic charges and/or FF atom types (or you can add them in a
2nd step using the "set" command of LEaP; see for instance

You can also use R.E.D. to
compute RESP (or ESP) charges and to generate a force field library in
the Tripos mol2 file format with a correct topology for your whole
molecule (or molecule fragment). R.E.D. does not differentiate
"organic" cases from others. Thus, it will work whatever is the metal
selected. So far, R.E.D.-III is fully compatible with chemical
elements up to Z=35, but we have implemented methods in R.E.D.-IV to
remove this limit.

Concerning the orbitals associated with a minimum containing a
transition metal there are indeed reports in the literature that such
a minimum exist in a particular electronic configuration. This is true
for heme. I do not know in your case, but my understanding is that the
problem of multiple multiplicities of iron is general. If you decide
to use R.E.D., your best bet is to try to find a correct minimum in a
standalone way, and characterize the orbitals of this minimum. Then,
when you "caught" this right minimum, load the QM output in R.E.D. as
an input in association with the corresponding p2n file, and you will
get as final output a tripos mol2 file (or a set of Tripos mol2 files
if you use several molecules as inputs).

regards, Francois

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