[MMTK] MMTK Bug in SubChain.replaceResidue

Talipov, Marat marat.talipov at marquette.edu
Thu Feb 24 23:43:59 UTC 2011

Dear Konrad,

It seems that the subroutine replaceResidue in class SubChain (Proteins.py, MMTK v2.7.3) contains a bug which causes a program crash. The issue is in lines 532 and 535, where the zeroth element of 'peptide_old' array is requested. This array is supposed to contain bonds of N and C peptide atoms of old residues. However, these atoms and corresponding bonds are removed just few lines above, so this array (at least sometimes) is empty. Here is a simple patch to fix this problem, which is attached to this message.

Sincerely yours,

Dr Marat R. Talipov
Postdoctoral Fellow
Department of Chemistry, Marquette University
Wehr Chemistry Building, P.O. Box 1881
Milwaukee, WI-53201
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