#============================================================*
#               test rigid body simulation of a loop         *
#                                                            *
# res 593-613                                                *
#                                                            *
# define domains consisting of peptide and sidechain groups. *
# use hinge joint.                                           *
#============================================================*

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

# open pdb file
database open name = db1  format = pdb  file = loop_piece.pdb

# read molecule
molecule read  name = m1   database = db1


domain create loop  = C
domain loop backbone color = [ 0.6 0.6 0.6 ] width = 1 show

domain create d1 = C[596-597]  peptide = true 
domain d1 bonds atoms = true atom_color = element \
                bond_color = [ 1 0 0 ]  render = line show 

domain create d2 = C[597]  sidechain_group = true 
domain d2 bonds atoms = true atom_color = [ 1 0.6 0 ] bond_color = [ 1 0.6 0 ] show
#--------------
domain create d3 = C[597-598]  peptide = true 
domain d3 bonds atoms = true atom_color = element   \
                render = line bond_color = [ 1 0 0 ]  show

domain create d4 = C[598]  sidechain_group = true 
domain d4 bonds atoms = true atom_color = [ 0 1 0 ] bond_color = [ 0 1 0 ] show
#--------------
domain create d5 = C[598-599]  peptide = true 
domain d5 bonds atoms = true atom_color = element  \
                render = line bond_color = [ 1 0 0 ]  show

domain create d6 = C[599]  sidechain_group = true 
domain d6 bonds atoms = true atom_color = [ 1 1 0 ] bond_color = [ 1 1 0 ] show

domain create d7 = C[599-600]  peptide = true
domain d7 bonds atoms = true atom_color = element  \
                render = line bond_color = [ 1 0 0 ]  show



#----------- add rigid bodies ------------------------------

body create  name = ground    type = ground
body create  name = d1b  type = rigid  domain = d1
body create  name = d2b  type = rigid  domain = d2
body create  name = d3b  type = rigid  domain = d3
body create  name = d4b  type = rigid  domain = d4
body create  name = d5b  type = rigid  domain = d5
body create  name = d6b  type = rigid  domain = d6
body create  name = d7b  type = rigid  domain = d7

#----------------- add joints ------------------------------

#----------- jnt 1 ---------------
#joint create  name = jnt1  type = weld domain = d1  res = C[596] use = C
joint create  name = jnt1  type = ball domain = d1  res = C[596] use = C
joint jnt1 color = [ 1 1 1 ] msize = 0.01 shading = color show = true
joint jnt1 bodies = { ground d1b }

#----------- jnt 2&3 ---------------
joint create  name = jnt2  type = hinge  position = d2:C[597]:N      \
              use_bond = true  bond = { d2:C[597]:CA  d1:C[597]:N }
#joint create  name = jnt2  type = weld position = d2:C[597]:N      
joint jnt2 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt2 bodies = { d1b d2b }

joint create  name = jnt3  type = hinge  position = d3:C[597]:C      \
              use_bond = true  bond = { d2:C[597]:CA  d3:C[597]:C }
#joint create  name = jnt3  type = ball position = d2:C[597]:C   
joint jnt3 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt3 bodies = { d2b d3b }

#----------- jnt 4 & 5 ---------------
joint create  name = jnt4  type = hinge  position = d4:C[598]:N      \
              use_bond = true  bond = { d3:C[598]:N  d4:C[598]:CA }
joint jnt4 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt4 bodies = { d3b d4b }

joint create  name = jnt5  type = hinge  position = d5:C[598]:C      \
              use_bond = true  bond = { d4:C[598]:CA  d5:C[598]:C }
joint jnt5 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt5 bodies = { d4b d5b }


#----------- jnt 6 & 7 ---------------
joint create  name = jnt6  type = hinge  position = d6:C[599]:N      \
              use_bond = true  bond = { d5:C[599]:N  d6:C[599]:CA }
joint jnt6 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt6 bodies = { d5b d6b }

joint create  name = jnt7  type = hinge  position = d7:C[599]:C      \
              use_bond = true  bond = { d6:C[599]:CA  d7:C[599]:C }
joint jnt7 color = [ 1 1 1 ] msize = 0.01 shading = flat  show = true
joint jnt7 bodies = { d6b d7b }



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

simulation create name = rsim  type = rigid

# add bodies
#-----------
simulation rsim add bodies = { ground d1b  d2b d3b d4b d5b d6b d7b }

# add joints
#-----------
simulation rsim add joints = { jnt1 jnt2 jnt3 jnt4 jnt5 jnt6 jnt7 }

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

# add forces
#-----------
force create  name = force1          \
              type = explicit        \
              point = [ 0 0 0 ]      \
              direction = [ 1.0 0 0 ]  \
              scale = 1.0

#simulation rsim add force = force1    \
                    body = d2b       \
                    time = { 0 1000 }

force create  name = force2          \
              type = explicit        \
              point = d3:C[597]:O    \
              global_frame = true    \
              direction = [ 0 -0.2 0 ]  \
              scale = 1.0

simulation rsim add force = force2    \
                    body = d3b       \
                    time = { 0 1000 }


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

simulation rsim time step = 0.001



graphics  center  point = [ 12.113 14.5242 5.90444 ]