[AMBER] How adding cluster to a model

From: Damiano Spadoni <enxds6.nottingham.ac.uk>
Date: Tue, 10 May 2016 11:57:14 +0000

Dear Ambers,

I am working on the pdb file of a protein model that is known having a metal cluster coordinated to three cysteine residues.
I've already got the library of the cluster and I changed the residues of interest from CYS to CYF according to xleap to allow the coordination bond between the cysteine sulfur and the metal atoms of the cluster.
As I don't have pdb coordinates for my cluster because the protein has been created through homology model (even if I could achieve them taken from the pdb of the crystal structure of a very similar protein), how can I parameterise in xleap this new system ProteinModel+cluster?
I know the usage of the bond command in xleap, but once I load the model pdb, it automatically put missing H atoms on the cysteine sulfur.

Any help would be greatly appreciated.

Damiano Spadoni

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Received on Tue May 10 2016 - 05:00:03 PDT
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