Hi groups,
I am using Xplor-nih to refine a small protein with two helical domains
and a loop connecting them. I am using NOE restaints and torsion angle
data.
When I analyze the final structure, I found that there are 1-2 residues
in the left hand helix region in the Ramachandran plot for a overall of
around ~50 structure. I use torsion angle dynamics and only use the
replusive vdw potential.
I do not have a lot of restraints in the loop region. I do not know
whether it is the reason I have those left handed helix. It is rare to see
the left handed though.
I do not know what I might have done wrong. Any help is greatly
appreciated.
Thanks,
Lei
