mcintosh at OTTER.BIOCHEM.UBC.CA
Sat Nov 9 23:25:38 EST 1996
I noticed recently that in many NMR structures
determined with XPLOR, the guanidino groups
of Arginine sidechains are not planar. That is,
they often show rotation about the Ne-Cz bond.
The problem arises because an improper angle is
commented out in the topallhdg.pro file, e.g.
! improper CZ NH1 HE NE ! planar HE, CZ
Removing the ! solves the problem (unless there is
some subtle reason why this was commented out? I noticed
it is commented out in the 3.8 release).
However, the resulting guanidino group appears to
be named "incorrectly" in that IUPAC convention
requires the Nn1 group to be "cis" to the Cd.
(eg see http://www.bmrb.wisc.edu/Nomenclature/commonaa.html).
This is easily corrected by specifying the improper angle
improper CZ NH2 HE NE ! planar HE, CZ
This appears to work but I would appreciate any feedback
if I have missed something.
University of British Columbia
mcintosh at otter.biochem.ubc.ca
More information about the X-plor