Ion coordination with peptide

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Ion coordination with peptide

Ekaterina
Dear, Molecular Modeling specialists and amateurs)

I wanted to try to simulate structure of little peptide which is contain cysteine zinc cluster. And till now cant'n find a way to add inorganic ions to the structure, after apploading of original amino acid chain.

Would be really thanksfull for advice
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Re: Ion coordination with peptide

Niki
Zinc is available in the AMBER force field, but not in the file \data\ForceField\FineType.mlm.
Probably the best way is to type it there, by analogy with Na+.

An easier way is to save the model in .hin format and add the line with the zinc.
In this case, you will be able to perform calculations in AMBER only and can not switch to a different force field, or return to .mlm format.
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Re: Ion coordination with peptide

Niki
In reply to this post by Ekaterina
Dear Ekaterina,

I've never worked with zinc, why it's not in the standard residues set.
If you tell what and how we can do with the zinc, we can to introduce its support together with you.
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Re: Ion coordination with peptide

Niki
In reply to this post by Ekaterina
Interesting article on modeling with zinc
http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm
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Re: Ion coordination with peptide

Ha Pea
Could you tell me how to change pH in abalone? thank you very much!
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Re: Ion coordination with peptide

Niki
Unfortunately it is not able.