AMBER Archive (2008)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Sep 16 2008 - 14:15:52 CDT

> addIons: Argument #2 is type String must be of type: [unit]

Your addIons cmd is wrong. Try 'desc <ion_unit>' to see what you are
using, and 'list' to see all the units that are available.

> WARNING: There is a bond of 7.224966 angstroms between:
> ------- .R<THR 304>.A<C 13> and .R<THR 305>.A<N 1>
> WARNING: There is a bond of 10.331638 angstroms between:
> ------- .R<VAL 1168>.A<C 15> and .R<ASP 1169>.A<N 1>
> WARNING: There is a bond of 25.906360 angstroms between:
> ------- .R<GLY 1182>.A<C 6> and .R<GLY 1183>.A<N 1>

Possibly you have multiple molecules in your pdb file without TER
cards between them?

> WARNING: There is a bond of 3.265214 angstroms between:
> ------- .R<F3S 1453>.A<S3 3> and .R<F3S 1453>.A<S4 4>
> WARNING: There is a bond of 3.432639 angstroms between:
> ------- .R<F3S 1453>.A<S2 2> and .R<F3S 1453>.A<S3 3>

Looks like you have some long bonds in your prep file - do these agree
with experiment?

> WARNING: The unperturbed charge of the unit: -8.000010 is not zero.

Maybe because addIons didn't work?
        
> Could not find bond parameter for: FE - FE
> Could not find bond parameter for: FE - FE
...
> Could not find angle parameter: FE - FE - FE

You have Fe-Fe bond(s). What does your current prep file look like?

> Could not find bond parameter for: S - FE
> Could not find angle parameter: S - S - FE

Params for S-Fe will be needed - find or derive some and add via a
frcmod file.

Bill
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