AMBER Archive (2008)

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

From: Hakkim Boy (vhakkim_at_yahoo.co.in)
Date: Mon Sep 15 2008 - 07:30:04 CDT

prepin file need the parameters like angle, torsion and bond length, we can collect this from optimized structure 

V. Hakkim

--- On Mon, 15/9/08, moitrayee_at_mbu.iisc.ernet.in <moitrayee_at_mbu.iisc.ernet.in> wrote:

From: moitrayee_at_mbu.iisc.ernet.in <moitrayee_at_mbu.iisc.ernet.in>
Subject: Re: AMBER: 3fe-4s cluster parameter file generation
To: amber_at_scripps.edu
Date: Monday, 15 September, 2008, 4:50 PM

Thank you very much for your reply. I did a single point gaussian calculation
and obtained the ESP charges. I prepared the .prepc file for the cluster and
ran
parmchk to generate the frcmod files. Everything is fine till loading of the
pdb
but then it asks for the parameters i had mentioned before.
The results of desc in leap is:

UNIT name: F3S
Head atom: .R<F3S 1>.A<S1 1>
Tail atom: .R<F3S 1>.A<FE3 7>
Contents:
R<F3S 1>
What should i do to modify the unit? Looking eagerly forward for a reply.

Sincere Regards,
Moitrayee

> On Mon, Sep 15, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:
>>
>> Could not find bond parameter for: FE - FE
>
>> But the parameters that are being asked are not involved in the
structure's
>> connectivity at all. There is no Fe-Fe bond at all in the
above-mentioned
>> cluster.
>
> How did you create the unit for the iron-sulfur cluster? You can use
> the "desc" command in leap to look at the bonds that are
defined. If
> you don't want an Fe-Fe bond, you will have to change the way that
unit
> is built in the first place.
>
> ...dac
>
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