AMBER Archive (2008)

Subject: Re: AMBER: Nonbonded FE parameter missing in frcmod.

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Sep 11 2008 - 12:16:34 CDT

I have searched the amber archives and found that some people have used
NONBON
Fe 1.2000 0.0500 (HEME)
My target is to look at the overall conformational changes in the protein and
not concentrating very much on the cluster itself. Is it advisable that i use
the parameters as from HEME for my system as well? Also i found that you have
been calculating the force fields for fe4s4 clusters. If you please suggest me
how to modify it for 3fe clusters.
Looking eagerly forward for your reply.
Thank you a lot.

Sincere Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore - 560012
India.

> On Thu, Sep 11, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
>>
>> I am trying to simulate a protein having [3fe-4s]+1 as a ligand.
>
> You are going to have to do work on your own here: antechamber does not
> support metal ions for automatic generation of force fields.
>
> My suggestion is to look for force fields for fe4s4 clusters, and then see
> if you can modify them for the 3fe clusters. Depending on what you are
> interested in (i.e. the properties of the cluster itself, or of the protein at
> distances far removed from the cluster?) you may need a fair amount of effort
> to get things set up.
>
> ...dac 

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