AMBER Archive (2009)

Subject: [AMBER] Re: Regd: Fe4S4

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Jun 22 2009 - 13:39:57 CDT

On Mon, Jun 22, 2009, KIRTANA S wrote:
> Hello Dr.David Case,

Please send amber-related questions to the mail reflector, amber_at_ambermd.org,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See
http://lists.ambermd.org/mailman/listinfo/amber for information on how to
subscribe.

>
> I found the parameter files for Fe4S4 cluster posted by you in AMBER archive
> .I am using the frcmod file for Fe4S4.
> When I try to build the structure ,my Fe4S4 cluster shows as terminated
> and I am unable to bond it with sulphur of my dendrimer arm (enclosing my
> Fes core).

You don't say (in any of your posts) exactly what commands you are using.
So that makes it hard to help. But your pdb files shows a single residue with
over 600 atoms, which will be a problem.

I also don't know which files you may have retrieved from the archive.
But they were probably designed to have the Fe4S4 group as its own residue,
then to use the "bond" command in LEaP to create bonds from the fe4s4 residue
to cysteine side chains of a protein. Try using this to construct an Fe4S4
protein (e.g. starting from the pdb file and leap.in script in the attached
tar file). That will show you what the design was, and should help you get
started towards your problem.

Note that the frcmod file expects the fe4s4 unit to be bonded to a cysteine
residue of a peptide. If you are going to bond this to some other moiety, you
will probably have to generate appropriate parameters, perhaps by analogy to
peptides.

...good luck...dac



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