[MMTK] Value Error: cyclic bond structure

tezcan at ecs.umass.edu tezcan at ecs.umass.edu
Tue Oct 27 18:29:56 UTC 2009

Hi all,
While trying to read phi/psi angles of some residues, I get the error  
"Value Error: cyclic bond structure". I am wondering why this might be  
happening, and if there is any way to overcome it. I ran in to this  
error in many residues of 1CBN and 2ERL. As an example:

from MMTK import *
from MMTK.Proteins import Protein, Residue
from MMTK.ForceFields import Amber99ForceField

universe = InfiniteUniverse(Amber99ForceField(mod_files=['frcmod.ff99SB']))
universe.protein = Protein("1CBN.pdb")

Thanks for your help,

More information about the mmtk mailing list