AMBER Archive (2009)

Subject: [AMBER] parameters Fe4S4 cluster

From: KIRTANA S (skirtana4_at_gmail.com)
Date: Sun Jun 21 2009 - 21:30:08 CDT

Dear Amber users,

In my model I have Fe-S core encapsulated in dendrimer (three generations)
arms which consists of ether linkages of benzene rings terminated with
carboxyl group .
I have considered each of my dendrimer arm as residues .For Fe4 S4 I have
used a separate pdb file and parameter file and when I load it into xleap
and try to sequence the two structures I get the following error :

desc D1
UNIT name: D1
Head atom: .R<FS4 1>.A<FE4 4>
Tail atom: .R<FS4 1>.A<FE1 1>
Contents:
R<FS4 1>
> desc D2
UNIT name: D2
Head atom: .R<MOL 1>.A<C710 170>
Tail atom: .R<MOL 1>.A<S13 64>
Contents:
R<MOL 1>

> q= sequence {D2 D1}
Sequence: D2
Sequence: D1
failed to find default bond length FE4-S13, types FS-sh
Joining MOL - FS4

Please suggest how should I go about .I really appreciate your help in this.

Thanks and Regards
Kirtana
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