AMBER Archive (2009)

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

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Thu Aug 06 2009 - 15:22:37 CDT

Hello Kirtana,

I have not used iron atoms in the GAFF force field. But I would back
up a step and take a close look at your output from antechamber
first. Are you trying to add very long, artificial bonds between iron
atoms in order to maintain a cubic structure? Or are those artifacts
from the bond type perception in antechamber?

The reason I ask is that depending on the valence that antechamber is
expecting for iron, it may create "extra" bonds that are not present
in the physical cubane system.

And is it just me, or is iron not listed in the original GAFF paper
(Wang et al, J Comp Chem, 2004)?

Hope these questions are helpful!

Best regards,
Nicholas Musolino

On Aug 6, 2009, at 4:09 PM, KIRTANA S wrote:

> Dear All,
> 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 in
> gaff.dat file , but it shows the following message :
>> 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.
> -- 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.
> I shall really appreciate you help in this .
> (P.S: It is a iron sulphur cluster FE4S4 cubane)
> Thanks and Regards
> Kirtana
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