#============================================================* # test restraints * # * # rebind nlobe of cam. * #============================================================* # set units units units scale name = mass uname = reducedMass value = 10000.0 # open pdb file #--------------- database open name = bneck format = pdb file = 1M45.pdb molecule read name = m2 database = bneck domain create bound = AB # open pdb file #--------------- database open name = neck format = pdb file = 1M46.pdb # read molecule #--------------- molecule read name = m1 database = neck molecule m1 xform transaltion = [ -2.01791 -3.05832 -0.54274 ] domain create hc = A # show all helices #----------------- #domains create helices = true prefix = h color = [ 1 0 0 ] \ width = 5 # show all sheets #---------------- #domains create sheets = true prefix = sh color = [ 0 1 1 ] width = 8 # create helix domains #--------------------- domain create h1 = A[3-15] #domain h1 backbone color = [ 1 0 0 ] width = 3 show domain create h2 = A[26-34] domain h2 backbone color = [ 1 0 0 ] width = 3 show domain create h3 = A[39-49] domain h3 backbone color = [ 1 0 0 ] width = 3 show domain create h4 = A[50-55] domain h4 backbone color = [ 1 0 0 ] width = 3 show domain create h5 = A[61-71] domain h5 backbone color = [ 1 0 0 ] width = 3 show domain create h6 = A[71-78] domain h6 backbone color = [ 1 0 0 ] width = 3 show domain create h7 = A[82-92] domain h7 backbone color = [ 1 0 0 ] width = 3 show # create sheet domains #--------------------- domain create sh = A[21-23,58-60] domain sh backbone color = [ 1 0 0 ] width = 3 show # create loop domains #-------------------- domain create loop1 = A[15-21] domain loop1 backbone color = [ 1 0 0 ] width = 3 show domain create loop2 = A[23-26] domain loop2 backbone color = [ 1 0 0 ] width = 3 show domain create loop3 = A[34-39] domain loop3 backbone color = [ 1 0 0 ] width = 3 show domain create loop4 = A[49-50] domain loop4 backbone color = [ 1 0 0 ] width = 3 show domain create loop5 = A[55-58] domain loop5 backbone color = [ 1 0 0 ] width = 3 show domain create loop6 = A[60-61] domain loop6 backbone color = [ 1 0 0 ] width = 3 show domain create loop7 = A[78-79] domain loop7 backbone color = [ 1 0 0 ] width = 3 show domain create loop7_1 = A[79-80] domain loop7_1 backbone color = [ 1 0 0 ] width = 3 show domain create loop7_2 = A[80-82] domain loop7_2 backbone color = [ 1 0 0 ] width = 3 show # create cam domains #-------------------- domain create camClobe = A[92-148] #domain create camClobe = A[82-148] #domain create camClobe = A[100-148] domain camClobe backbone color = [ 1 0 0 ] width = 3 show # create iq domain #-------------------- domain create iq = B #domain iq backbone color = [ 0.6 0.6 0.6 ] width = 3 show # fit bound cam model #-------------------- domain bound fit sequence = B[814-817] \ destination = iq \ destination_sequence = B[862-865] \ atom_names = { O C CA } #domain bound backbone name = fit color = [ 1 1 1 ] width = 3 show #domain bound backbone color = [ 0.5 0.5 0.5 ] width = 1 show #--------------------------------------------------------------# # create bodies # #--------------------------------------------------------------# body create name = ground type = ground body create name = h1Body type = rigid domain = h1 body create name = h2Body type = rigid domain = h2 body create name = h3Body type = rigid domain = h3 body create name = h4Body type = rigid domain = h4 body create name = h5Body type = rigid domain = h5 body create name = h6Body type = rigid domain = h6 body create name = h7Body type = rigid domain = h7 body create name = l1Body type = rigid domain = loop1 body create name = l2Body type = rigid domain = loop2 body create name = l3Body type = rigid domain = loop3 body create name = l4Body type = rigid domain = loop4 body create name = l5Body type = rigid domain = loop5 body create name = l6Body type = rigid domain = loop6 body create name = l7Body type = rigid domain = loop7 body create name = l71Body type = rigid domain = loop7_1 body create name = l72Body type = rigid domain = loop7_2 body create name = shBody type = rigid domain = sh body create name = camClobeBody type = rigid domain = camClobe body create name = boundBody type = static domain = bound #--------------------------------------------------------------# # create joints # #--------------------------------------------------------------# joint create name = groundJnt type = weld position = [ 0 0 0 ] joint groundJnt bodies = { ground camClobeBody } joint create name = h1L1Jnt type = weld domain = hc res = A[15] use = CA joint h1L1Jnt color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint h1L1Jnt bodies = { h1Body l1Body } joint create name = L1ShJnt type = weld domain = hc res = A[21] use = CA joint L1ShJnt color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint L1ShJnt bodies = { l1Body shBody } joint create name = ShL2Jnt type = weld domain = hc res = A[23] use = CA joint ShL2Jnt color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint ShL2Jnt bodies = { shBody l2Body } joint create name = L2H2Jnt type = weld domain = hc res = A[26] use = CA joint L2H2Jnt color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint L2H2Jnt bodies = { l2Body h2Body } joint create name = H2L3Jnt type = weld domain = hc res = A[34] use = CA joint H2L3Jnt color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint H2L3Jnt bodies = { h2Body l3Body } joint create name = L3H3Jnt type = weld domain = hc res = A[39] use = CA joint L3H3Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L3H3Jnt bodies = { l3Body h3Body } joint create name = H3L4Jnt type = weld domain = hc res = A[49] use = CA joint H3L4Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint H3L4Jnt bodies = { h3Body l4Body } joint create name = L4H4Jnt type = weld domain = hc res = A[50] use = CA joint L4H4Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L4H4Jnt bodies = { l4Body h4Body } joint create name = H4L5Jnt type = weld domain = hc res = A[55] use = CA joint H4L5Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint H4L5Jnt bodies = { h4Body l5Body } joint create name = L5SHJnt type = weld domain = hc res = A[58] use = CA joint L5SHJnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L5SHJnt bodies = { l5Body shBody } joint create name = SHL6Jnt type = weld domain = hc res = A[60] use = CA joint SHL6Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint SHL6Jnt bodies = { shBody l6Body } joint create name = L6H5Jnt type = weld domain = hc res = A[61] use = CA joint L6H5Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L6H5Jnt bodies = { l6Body h5Body } joint create name = H5H6Jnt type = ball domain = hc res = A[71] use = CA joint H5H6Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint H5H6Jnt bodies = { h5Body h6Body } joint create name = H6L7Jnt type = ball domain = hc res = A[78] use = CA joint H6L7Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint H6L7Jnt bodies = { h6Body l7Body } joint create name = L7L71Jnt type = ball domain = hc res = A[79] use = CA joint L7L71Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L7L71Jnt bodies = { l7Body l71Body } joint create name = L71L72Jnt type = ball domain = hc res = A[80] use = CA joint L71L72Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L71L72Jnt bodies = { l71Body l72Body } joint create name = L72H7Jnt type = ball domain = hc res = A[82] use = CA joint L72H7Jnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint L72H7Jnt bodies = { l72Body h7Body } joint create name = H7CamJnt type = ball domain = hc res = A[92] use = CA joint H7CamJnt color = [ 1 0 0 ] msize = 0.05 shading = color show = true joint H7CamJnt bodies = { h7Body camClobeBody } #--------------------------------------------------------------# # create a rigid simulation # #--------------------------------------------------------------# simulation create name = rsim type = rigid # add bodies #----------- simulation rsim add bodies = { ground h1Body h2Body h3Body h4Body h5Body h6Body \ h7Body l1Body l2Body l3Body l4Body l5Body l6Body \ l7Body l71Body l72Body shBody camClobeBody } # add joints #----------- simulation rsim add joints = { h1L1Jnt L1ShJnt ShL2Jnt L2H2Jnt H2L3Jnt \ L3H3Jnt H3L4Jnt L4H4Jnt H4L5Jnt L5SHJnt SHL6Jnt \ L6H5Jnt H5H6Jnt H6L7Jnt L7L71Jnt L71L72Jnt L72H7Jnt \ H7CamJnt } # set solver #----------- simulation rsim solver = ode simulation rsim solver finite_rotation = on # add random forces #------------------ force create name = force1 \ type = random \ mean = 0.0 \ sd = 8.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force1 \ body = h1Body \ time = { 0 1000 } #------------------ force create name = force2 \ type = random \ mean = 0.0 \ sd = 20.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force2 \ body = camClobeBody \ time = { 0 1000 } #------------------ force create name = force3 \ type = random \ mean = 0.0 \ sd = 8.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force3 \ body = h2Body \ time = { 0 1000 } #------------------ force create name = force4 \ type = random \ mean = 0.0 \ sd = 8.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force4 \ body = h3Body \ time = { 0 1000 } #------------------ force create name = force5 \ type = random \ mean = 0.0 \ sd = 2.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force5 \ body = h4Body \ time = { 0 1000 } #------------------ force create name = force6 \ type = random \ mean = 0.0 \ sd = 8.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force6 \ body = h5Body \ time = { 0 1000 } #------------------ force create name = force7 \ type = random \ mean = 0.0 \ sd = 4.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force7 \ body = h6Body \ time = { 0 1000 } #------------------ force create name = force8 \ type = random \ mean = 0.0 \ sd = 4.0 \ seed = 147321 \ scale = 0.1 simulation rsim add force = force8 \ body = h7Body \ time = { 0 1000 } # initialize simulation #---------------------- simulation rsim momentum = off simulation rsim initialize simulation rsim time step = 0.02 #simulation state save_frequency = 10 graphics background color = [ 1 1 1 ]