> hi everyone
>
> Does anyone have the topology parameters for Fe-S cluster ?
>
> Subarna
Hi,
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).
tleap.in 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
fs4.in 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: tleap.in
- chemical/x-mopac-input attachment: fs4.dat
- application/octet-stream attachment: fs4.in
Received on Mon Jul 06 2009 - 12:19:19 PDT
