[AMBER] iron sulphur cluster parametrization

From: Francesco Oteri <francesco.oteri.gmail.com>
Date: Sat, 29 Oct 2011 10:39:52 +0200

Dear AMBER users,
I have to simulate a protein made by three iron sulphur cluster, namely
one 4Fe4S, one "canonical" 3Fe4S and one "not-canonical" 3Fe4S.
The topic of the research is the caracterization of the overall protein
structure, so I don't need an accurate representation of the clusters.
Although I found CHARMM parameters for the 4Fe4S and 3Fe3S clusters, I
prefer using AMBER-ILDN force-field. Comparisons with other force-fields
show that AMBER-ILDN is the best parameter set to describe protein features.

So regarding my protein, I guess I can use AMBER for protein. For the
iron-sulphur clusters it is enough constraining
bonds,angles and dihedrasl among the S and Fe atoms. The problem are
atomic charges.

I've been running GAMESS-US, both as stand-alone and RED-server, but it
fails to converge both with or without geometry optimization.
I am using the BLYP/6-31+G* model.

I've three main questions to address:
1) Has anyone some input file suitable for the RESP-charges calculation
2) Is there any simple rule, or a software, that can help me to
calculate iron multiplicity for iron containing molecules?
3) Are parameters for the 3Fe4S avalaible for the AMBER force-field?

Any advice doesn't contained in the above questions is well apreciated.



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Received on Sat Oct 29 2011 - 02:00:03 PDT
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