AMBER Archive (2008)

Subject: Re: AMBER: 3fe-4s cluster parameter file generation

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 17 2008 - 06:26:07 CDT

On Wed, Sep 17, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:

> I have manually prepared the prepc file from my gaussian single point energy
> calculation. I have taken the standard orientation of the gout file and the
> ESP charges and prepared the prepc file. I really dont know how to manage
> this thing and i am getting unwanted bonds in my ligand.

This is not a problem that is likely to be easily solved by email. I've
had an "on-again, off-again" project for several years to make a useful
force field for fe4s4 systems, and my approach (at least) requires a
pretty detailed knowledge of the underlying file formats. The Fe3S4
problem is probably even more difficult.

I'm assuming you've scoured the literature (checking, e.g. papers by
Toshiko Ichiye and others) for clues here. But basically, it's a lot of
work, and it's unlikely that just posting your problems to the mailing
list will be very productive. You might start with the mol2 format
(rather than prep), since that makes it easier to specify exactly
which bonds you want. And, I'd recommend starting with simpler things
like rubredoxin, then move up to Fe2S2 clusters, before tackling the
bigger systems.

....dac

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