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<DIV><FONT face=Arial size=2><SPAN
class=719294519-20052011>Hello,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=719294519-20052011></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=719294519-20052011>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?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=719294519-20052011></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=719294519-20052011>Frank
Neuhaus</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=719294519-20052011>Northwestern
Univ.</SPAN></FONT></DIV></BODY></HTML>