#============================================================#
#          test rigid body simulation of a helix             #
#                                                            #
# define rigid bodies for peptide plane and sidechains.      #
#============================================================#

system echo = off
system verbose = false

# set units
#----------
#units
units scale  name = mass   uname = reducedMass   value = 10000.0

# open pdb file
#--------------
database open name = db1  format = pdb  file = ../data/neck_xform.pdb

# read molecule
#--------------
molecule read  name = m1   database = db1

# create helix domain
#--------------------
domain create helix = C[780-790]
domain helix backbone color = [ 1 1 1 ]  width = 3 show
domain helix bonds atoms = true  atom_color = element  bond_color = [ 0 1 0 ] show 


domain helix hbonds color = [ 0 1 0 ]  width = 1 show

graphics  center  domain = helix