#============================================================*
#               test reading 2nd structure                   *
#                                                            *
# create multibody from secondary strucutre.                 *
#============================================================*

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

# open pdb file
database open name = db1  format = pdb  file = ../data/1W7I.pdb

# read molecule
molecule read  name = m1   database = db1  

# create a some domains
#-------------------
domain create head = A[2-780]
domain head backbone color = [ 0.6 0.6 0.6 ] width = 1 show


# create multibody
#-----------------

domain create headModel_1 = A[60-381]
multibody  create  name = hm1b  domain = headModel_1  type = secondary_structure 

domain create headModel_2 = A[386-594]
multibody  create  name = hm2b  domain = headModel_2  type = secondary_structure 

domain create headModel_3 = A[632-792]
multibody  create  name = hm2b  domain = headModel_3  type = secondary_structure 



body create  name = ground    type = ground

joint create  name = groundJnt  type = ball domain = hm1b_helix1  res = A[65] use = CA
joint groundJnt color = [ 1 1 1 ] msize = 0.02 shading = color show = true
joint groundJnt bodies = { ground hm1b_helix1Body }


#--------------------------------------------------------------#
#                 create a rigid simulation                    #
#--------------------------------------------------------------#

simulation create name = rsim  type = rigid

simulation rsim add bodies = all
simulation rsim add joints = all

# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on

# add forces
#-----------

force create  name = force2             \
              type = explicit           \
              point = [ 0 0 0 ]   \
              direction = [ 0 0 10.2 ]  \
              scale = 1.0

simulation rsim add force = force2    \
                    body =  hm1b_loop7Body \
                    time = { 0 1000 }


# initialize simulation
#----------------------
simulation rsim initialize

simulation rsim time step = 0.01