AMBER Archive (2008)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Sep 15 2008 - 09:15:12 CDT

On Mon, Sep 15, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:

> I did not use antechamber but manually did it using the co-ordinate and charge
> information from the Gaussian single point calculation. The prepc file is given
> below:
>
> 0 0 2
>
> This is a remark line
> molecule.res
> F3S XYZ 0
> CHANGE OMIT DU BEG
> 0.0000
> 1 DUMM DU M 999.000 999.0 -999.0 .00000
> 2 DUMM DU M 999.000 -999.0 999.0 .00000
> 3 DUMM DU M -999.000 999.0 999.0 .00000
> 4 S1 S M 0.402592 -1.514288 -1.117435 -0.15436
> 5 S2 S M -1.882611 0.670231 -0.727350 -0.17413
> 6 S3 S M 0.078709 -0.205500 1.731896 -0.31438
> 7 S4 S M 1.046182 1.057400 -1.309825 -0.13664
> 8 FE1 FE M -1.129336 -1.094156 0.156620 0.63632
> 9 FE2 FE M 1.553155 -0.302094 0.294594 0.59276
> 10 FE3 FE M -0.205279 1.391423 0.424303 0.55042

The above is wrong: you have every atom as a "mainchain" atom, so the
covalent structure implied above is S1-S2-S3-S4-Fe1-Fe2-Fe3, which is,
of course, not what you want.

...dac

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