AMBER Archive (2009)

Subject: RE: [AMBER] Regd : gaff force field

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 06 2009 - 15:42:14 CDT

Hi Kirtana,

> I am using gaff force field to generate the topology and parameter file
> for
> my model whuihc consists of Iron -sulphur cluster .
> Can anybody tell me what atom type should I use for iron . I used FE as

I would be VERY wary of using GAFF for iron sulphur clusters. This is way
outside of what it was designed to do. I suggest checking the literature to
see what others have done since I know numerous people have looked at such
systems in the past.

> > saveamberparm u dendron.inpcrd dendron.prmtop
> Checking Unit.
> WARNING: There is a bond of 89.489923 angstroms between:
> ------- .R<T111 1>.A<S1 11> and .R<FS4 45>.A<FE3 3>
> WARNING: There is a bond of 47.863802 angstroms between:
> ------- .R<T111 12>.A<S1 11> and .R<FS4 45>.A<FE4 4>
> WARNING: There is a bond of 12.355854 angstroms between:
> ------- .R<T111 23>.A<S1 11> and .R<FS4 45>.A<FE1 2>
> WARNING: The unperturbed charge of the unit: -1.996800 is not zero.

Looks to me like missing TER cards or a messed up initial structure. Bonds
of 89 angstroms are not good! You need to check your initial structure and
bonding carefully.
 
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> For atom: .R<FS4 45>.A<FE1 1> Could not find type: FE
> For atom: .R<FS4 45>.A<FE1 2> Could not find type: FE
> For atom: .R<FS4 45>.A<FE3 3> Could not find type: FE
> For atom: .R<FS4 45>.A<FE4 4> Could not find type: FE
> Parameter file was not saved.

You need to provide a frcmod file containing the parameters for Iron and
probably for the sulphur as well. If you tried to use antechamber it
probably quit with an error and never actually produced the files you need.
I suggest looking for parameters in the literature.

Good luck,
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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