AMBER Archive (2009)

Subject: [AMBER] Regd : gaff force field

From: KIRTANA S (skirtana4_at_gmail.com)
Date: Thu Aug 06 2009 - 15:09:14 CDT

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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