#============================================================*
#         for picture of contact geometry.                   *
#============================================================*

system echo = off
system verbose = false


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

# open pdb file
#--------------
database open name =  neck_xform  format = pdb file =  neck_xform.pdb

# read molecule
#--------------
molecule read  database =  neck_xform  name = m1  model = 1  type = protein

# create domains
#---------------
domain create hc = C


domain create iq2 = BC[788-814]
domain iq2 backbone color = [ 0.7 0 0 ] width = 6 show
domain create iq2cam = B
#domain iq2cam bonds  atom_color = [ 0.7 0 0 ] bond_color = [  0.7 0 0 ] \
                     atoms = false show = true


domain create iq3 = DC[814-836]
domain iq3 backbone color = [ 0 0.7 0 ] width = 6 show

domain create iq3h = C[814-836]
#domain iq3h bonds  atom_color = [ 0 0.7 0 ] bond_color = [ 0 0.7 0 ] \
                   atoms = true show = true

domain create iq3cam = D

#domain iq3cam bonds  atom_color = [ 0 0.7 0 ] bond_color = [ 0 0.7 0 ] \
                     atoms = true show = true


# 1st group
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 simulation
#------------------
simulation create name = rsim  type = rigid


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


# add interaction potentials
#---------------------------

domain iq3 define region = iq3_rgn  residues = D[90-140] 
#domain iq3 define region = iq3_rgn  residues = D[125-135] use_sidechains = true
#domain iq2 define region = iq2_rgn  residues = B[120-140] 
domain iq2 define region = iq2_rgn  residues = B

domain create iq3_region =  D[125-135] 
#domain iq3_region  bonds atoms = true bond_color = element show 

body iq3_body add potential = iq3_contact        \
                  type = contact                 \
                  region = iq3_rgn               \ 
                  sidechains = true              \ 
                  geometry = sphere              \
                  strength = 20.0                \
                  color = [ 1 0 1 ]              \
                  display = line                 \
                  width = 2                      \
                  show = true               

body iq2_body add potential = iq2_contact        \
                  type = contact                 \
                  region = iq2_rgn               \
                  geometry = ellipsoid           \
                  strength = 20.0                \
                  color = [ 1 0 1 ]              \
                  display = line                 \
                  width = 2                      \
                  show = true                    

simulation rsim add interaction = contact1                      \
                    body1 = iq3_body  potential1 = iq3_contact  \ 
                    body2 = iq5_body  potential2 = iq5_contact  \ 
                    time = { 0.0 10.0 }


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


# step simulation
#----------------
#simulation rsim step = 200


graphics background  color = [ 1 1 1 ]
graphics scale = 2.0