AMBER Archive (2009)

Subject: Re: [AMBER] Fe-S topology

From: Markus Kaukonen (
Date: Tue Jun 30 2009 - 02:28:51 CDT

> hi everyone
> Does anyone have the topology parameters for Fe-S cluster ?
> Subarna

I attach some files to start with.
These are unfortunately with old style prep files.
Those were used in
Kaukonen, M.; Söderhjelm, P.; Heimdal, J.; Ryde, U. Journal of
Chemical Theory and Computation 2008, 4, 985–1001.

Note that this is now optimised for F4S4 in [Ni, Fe] hydrogenase where
it has four CYM neighbors.
The total charge of the bare FS4 cluster is not integer (but it is -2
for FS4 + 4CYM system).
If I remember correctly (did this 2-3 years ago) you have to change
the order of atoms in the
Fe4S4 cluster to
get leap work correctly (you can figure this out by looking at the pdb
coordinates I send you).  a sample input file for tleap
fs4.pdb   pdb coord of Fe4S4 cluster
fs4_and4cym.pdb  pdb coord of Fe4S4 cluster and 4 CYM
fs4.dat AMBER parameter file AMBER prep file

Hope this helps, I take no responsibility for my possible errors.

If I remember correctly charges are not according to
amber-recommendation, but are turbomole ridft-bp-(6-31G*,DZP) esp
charges in vacuum using Merz-Kollmann radii for atoms.

Terveisin, Markus

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  • application/octet-stream attachment:

  • chemical/x-pdb attachment: fs4.pdb

  • chemical/x-mopac-input attachment: fs4.dat

  • application/octet-stream attachment:

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