#============================================================*
#                test universal joints                       *
#============================================================*

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

# read molecule 
#--------------
database open name = neck   format = pdb  file = neck_xform.pdb
molecule read  name = protein  database = neck

# create domains
#---------------
domain create hc = C
domain hc  backbone  color = [ 0.6 0.6 0.6 ] width = 2 show
domain create iq1 = AC[760-788]
domain iq1 backbone color = [ 1 0 0 ] width = 2 show
domain iq1 atoms color = [ 1 0 0 ] show

domain create iq1h = C[760-788]
domain iq1h atoms color = [ 1 0 0 ] show

domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0 1 0 ] width = 2 show
domain iq2 atoms color = [ 0 1 0 ] render = line show
domain create iq2h = C[788-814]
domain iq2h atoms color = [ 0 1 0 ] render = line show

domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0 1 ] width = 2 show
domain iq3 atoms color = [ 0 0 1 ] render = solid show


# create bodies from domains
#---------------------------
body create  name = ground    type = ground
body create  name = iq1_body  type = rigid   domain = iq1
body create  name = iq2_body  type = rigid   domain = iq2
body create  name = iq3_body  type = rigid   domain = iq3

# create joints 
#--------------

# 1st joint 
# ---------
#joint create  name = jnt1   type = universal position = hc:C[760]:CA   \
              use_pca = true  pca_res = hc:C[760-775]                  \
              axis1 = pca2  axis2 = pca3                               \
              force_const1 = 20.0  force_const2 = 20.0

#joint create  name = jnt1   type = universal position = hc:C[760]:CA   \
              use_pca = true  pca_domain = hc  pca_res = C[760-775]    \
              axis1 = pca2  axis2 = pca3                               \
              force_const1 = 20.0  force_const2 = 20.0

joint create  name = jnt1   type = universal domain = hc  res = C[760]  use = CA \
              use_pca = true pca_res = C[760-775]  axis1 = pca2  axis2 = pca3  \
              force_const1 = 20.0  force_const2 = 20.0

joint jnt1 bodies = { ground iq1_body }