[MMTK] Protein mutation: atomic coordinates of substituting residue

Talipov, Marat marat.talipov at marquette.edu
Tue Feb 22 21:13:45 UTC 2011

Dear Konrad,

I’d like to replace a cysteine residue in the peptide chain by the non-standard residue (which is S-nitrosated cysteine). There is a special function in MMTK for this purpose, named ReplaceResidue(). However it modifies only logical structure of protein thus leaving positions of ‘new’ atoms undefined.

In mailing list archive, I found a message (http://starship.python.net/pipermail/mmtk/2005/000920.html) where this problem was overcome. However that scripts seems to be not working on the most recent versions of MMTK (I got 2.7.3).  In any case, it was a manual way of solution.

Is there some way to automatically place atoms of substituting/mutating residue (whose geometry is defined in Database by a Z-Matrix) in correct positions in a protein?

Sincerely yours,

Dr Marat R. Talipov
Research Scholar

Department of Chemistry
Marquette University
Wehr Chemistry Building
P.O. Box 1881
Milwaukee, WI-53201

Phone: +1 414 477 6081
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