[gmx-users] re: ciis peptide linkage

Frank Neuhaus f-neuhaus at northwestern.edu
Fri May 20 22:04:35 CEST 2011

In the process of simulating my protein, I find three residues that don't
"behave"  Notes indicate an unusual bond.  I am finding out that the peptide
bonds in the fragment containing these residues are linked by cis-peptide
linkages.  Does Gromacs have difficulty with the rare cis peptide bond in a
protein?   It reports "unusual bond between e.g. 193(protein) and 194(none)
and the VMD viewer places the residue to the side of the box.  Any thoughts?
Frank Neuhaus
Northwestern Univ.
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