[gmx-users] re: ciis peptide linkage
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?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users