#============================================================* # test rigid body simulation of a loop * # * # res 593-613 * # * # define ball joints btw every two residues. * #============================================================* # 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[593-594] domain d1 backbone color = [ 1 0 0 ] width = 3 show #domain d1 bonds atoms = true atom_color = [ 1 0 0 ] bond_color = [ 1 0 0 ] \ atom_render = line show domain create d2 = C[594-595] domain d2 backbone color = [ 0 1 0 ] width = 3 show #domain d2 bonds atoms = true atom_color = [ 0 1 0 ] bond_color = [ 0 1 0 ] show domain create d3 = C[595-596] domain d3 backbone color = [ 0 0 1 ] width = 3 show #domain d3 bonds atoms = true atom_color = [ 0 0 1 ] bond_color = [ 0 0 1 ] show domain create d4 = C[596-597] domain d4 backbone color = [ 1 0 1 ] width = 3 show #domain d4 bonds atoms = true atom_color = [ 1 0 1 ] bond_color = [ 1 0 1 ] show domain create d5 = C[597-598] domain d5 backbone color = [ 1 1 0 ] width = 3 show domain d5 bonds atoms = true atom_color = [ 1 1 0 ] bond_color = [ 1 1 0 ] show domain create d6 = C[598-599] domain d6 backbone color = [ 1 0 0 ] width = 3 show domain create d7 = C[599-600] domain d7 backbone color = [ 0 1 0 ] width = 3 show domain create d8 = C[600-601] domain d8 backbone color = [ 0 1 0 ] width = 3 show domain create d9 = C[601-602] domain d9 backbone color = [ 0 0 1 ] width = 3 show domain create d10 = C[602-603] domain d10 backbone color = [ 1 0 1 ] width = 3 show domain create d11 = C[603-604] domain d11 backbone color = [ 0 1 1 ] width = 3 show domain create d12 = C[604-605] domain d12 backbone color = [ 1 1 0 ] width = 3 show domain create d13 = C[605-606] domain d13 backbone color = [ 1 0 0 ] width = 3 show domain create d14 = C[606-607] domain d14 backbone color = [ 0 1 0 ] width = 3 show domain create d15 = C[607-608] domain d15 backbone color = [ 1 1 0 ] width = 3 show domain create d16 = C[608-609] domain d16 backbone color = [ 0 0 1 ] width = 3 show domain create d17 = C[609-610] domain d17 backbone color = [ 0 1 1 ] width = 3 show domain create d18 = C[610-611] domain d18 backbone color = [ 1 0 0 ] width = 3 show domain create d19 = C[611-612] domain d19 backbone color = [ 1 0 1 ] width = 3 show domain d19 bonds atoms = true atom_color = [ 1 0 1 ] bond_color = [ 1 0 1 ] show domain create d20 = C[612-613] domain d20 backbone color = [ 0 0 1 ] width = 3 show domain d20 bonds atoms = true atom_color = [ 0 0 1 ] bond_color = [ 0 0 1 ] show #--------------------------------------------------------------# # create 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 body create name = d8b type = rigid domain = d8 body create name = d9b type = rigid domain = d9 body create name = d10b type = rigid domain = d10 body create name = d11b type = rigid domain = d11 body create name = d12b type = rigid domain = d12 body create name = d13b type = rigid domain = d13 body create name = d14b type = rigid domain = d14 body create name = d15b type = rigid domain = d15 body create name = d16b type = rigid domain = d16 body create name = d17b type = rigid domain = d17 body create name = d18b type = rigid domain = d18 body create name = d19b type = rigid domain = d19 body create name = d20b type = rigid domain = d20 joint create name = jnt1 type = ball domain = d1 res = C[593] use = CA joint jnt1 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt1 bodies = { ground d1b } joint create name = jnt2 type = ball domain = d1 res = C[594] use = CA joint jnt2 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt2 bodies = { d1b d2b } joint create name = jnt3 type = ball domain = d2 res = C[595] use = CA joint jnt3 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt3 bodies = { d2b d3b } joint create name = jnt4 type = ball domain = d3 res = C[596] use = CA joint jnt4 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt4 bodies = { d3b d4b } joint create name = jnt5 type = ball domain = d4 res = C[597] use = CA joint jnt5 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt5 bodies = { d4b d5b } joint create name = jnt6 type = ball domain = d5 res = C[598] use = CA joint jnt6 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt6 bodies = { d5b d6b } joint create name = jnt7 type = ball domain = d6 res = C[599] use = CA joint jnt7 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt7 bodies = { d6b d7b } joint create name = jnt8 type = ball domain = d7 res = C[600] use = CA joint jnt8 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt8 bodies = { d7b d8b } joint create name = jnt9 type = ball domain = d8 res = C[601] use = CA joint jnt9 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt9 bodies = { d8b d9b } joint create name = jnt10 type = ball domain = d9 res = C[602] use = CA joint jnt10 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt10 bodies = { d9b d10b } joint create name = jnt11 type = ball domain = d10 res = C[603] use = CA joint jnt11 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt11 bodies = { d10b d11b } joint create name = jnt12 type = ball domain = d11 res = C[604] use = CA joint jnt12 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt12 bodies = { d11b d12b } joint create name = jnt13 type = ball domain = d12 res = C[605] use = CA joint jnt13 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt13 bodies = { d12b d13b } joint create name = jnt14 type = ball domain = d13 res = C[606] use = CA joint jnt14 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt14 bodies = { d13b d14b } joint create name = jnt15 type = ball domain = d14 res = C[607] use = CA joint jnt15 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt15 bodies = { d14b d15b } joint create name = jnt16 type = ball domain = d15 res = C[608] use = CA joint jnt16 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt16 bodies = { d15b d16b } joint create name = jnt17 type = ball domain = d16 res = C[609] use = CA joint jnt17 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt17 bodies = { d16b d17b } joint create name = jnt18 type = ball domain = d17 res = C[610] use = CA joint jnt18 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt18 bodies = { d17b d18b } joint create name = jnt19 type = ball domain = d18 res = C[611] use = CA joint jnt19 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt19 bodies = { d18b d19b } joint create name = jnt20 type = ball domain = d19 res = C[612] use = CA joint jnt20 color = [ 1 1 1 ] msize = 0.01 shading = color show = true joint jnt20 bodies = { d19b d20b } #--------------------------------------------------------------# # create a rigid simulation # #--------------------------------------------------------------# simulation create name = rsim type = rigid # add bodies #----------- simulation rsim add bodies = { ground d1b d2b d3b d4b d5b d6b d7b d8b \ d9b d10b d11b d12b d13b d14b d15b d16b \ d17b d18b d19b d20b } # add joints #----------- simulation rsim add joints = { jnt1 jnt2 jnt3 jnt4 jnt5 jnt6 jnt7 jnt8 jnt9 jnt10 \ jnt11 jnt12 jnt13 jnt14 jnt15 jnt16 jnt17 jnt18 \ jnt19 jnt20 } # 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 = [ 0.1 0 0 ] \ scale = 1.0 simulation rsim add force = force1 \ body = d20b \ time = { 0 1000 } # initialize simulation #---------------------- simulation rsim initialize simulation rsim time step = 0.001 graphics center point = [ 12.0688 14.505 5.9047 ]