[MMTK] replaceResidue

Talipov, Marat marat.talipov at marquette.edu
Tue Jun 14 22:14:46 UTC 2011


Dear Konrad,


I'd like to extend replaceResidue subroutine so it could generate coordinates for the atoms of the new residue, so one could easily mutate any residue in a peptide chain.   

My idea is to store the residue coordinates in a Z-matrix format in the database and use them
to calculate the Cartesian coordinates using positions of the backbone atoms (say, CA,C,N) as a reference.

However, I'm not sure what is the best place to keep Z-matrix coordinates of residues. I thought about XXX_sidechain file,
but I got an error "name 'ZMatrix' is not defined".

I was wondering if you could give a couple of hints how should I proceed? 

Thanks a lot!


---

Dr Marat R. Talipov
Postdoctoral Fellow

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

Phone: +1 414 477 6081






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