/**************************************************************************** * Macromolecule parser error handling 28: Complex rate rule references * non-existent table. * * Expect an error regarding the line: * (camkii_subunit) + cam <-> (camkii_subunitB) [> COMPLEX_RATE cam ... * * Author: Jed Wing * Date: 2008-04-04 ****************************************************************************/ dt = 1e-6 iterations=1250000 sprintf(seed_str,"%04g",SEED) INCLUDE_FILE="parameters.mdl" TIME_STEP = dt ITERATIONS = iterations GRID_DENSITY = 15000 ACCURATE_3D_REACTIONS = FALSE PARTITION_X = [[-0.5001 TO 0.50001 STEP 0.02]] PARTITION_Y = [[-0.5001 TO 0.50001 STEP 0.02]] PARTITION_Z = [[-0.5001 TO 0.50001 STEP 0.02]] DEFINE_MOLECULES { camkii_subunit { DIFFUSION_CONSTANT_3D = 0 } camkii_subunitB { DIFFUSION_CONSTANT_3D = 0 } count_proxy_00 { DIFFUSION_CONSTANT_3D = 0 } count_proxy_01 { DIFFUSION_CONSTANT_3D = 0 } count_proxy_10 { DIFFUSION_CONSTANT_3D = 0 } count_proxy_11 { DIFFUSION_CONSTANT_3D = 0 } cam { DIFFUSION_CONSTANT_3D = cam_diffusion } } DEFINE_COMPLEX_MOLECULE camkii { NUMBER_OF_SUBUNITS = [2, 6] SUBUNIT[1:2, 1:6] = count_proxy_00 SUBUNIT[ 1, 2:4] = camkii_subunit SUBUNIT[1:2, 1:3] = camkii_subunit SUBUNIT[1:2, 5] = camkii_subunit SUBUNIT[ 1, 6] = camkii_subunitB SUBUNIT[ 2, 6] = camkii_subunitB SUBUNIT[ 2, 4] = camkii_subunitB SUBUNIT[1:2, 1:6] = camkii_subunit SHAPE { SUBUNIT[1, 1] = [-.0100, .00000, .0050] SUBUNIT[1, 2] = [ .0050, .00866, .0050] SUBUNIT[1, 3] = [ .0050, .00866, .0050] SUBUNIT[1, 4] = [ .0100, .00000, .0050] SUBUNIT[1, 5] = [ .0050, -.00866, .0050] SUBUNIT[1, 6] = [-.0050, -.00866, .0050] SUBUNIT[2, 1] = [-.0100, .00000, -.0050] SUBUNIT[2, 2] = [-.0050, .00866, -.0050] SUBUNIT[2, 3] = [ .0050, .00866, -.0050] SUBUNIT[2, 4] = [ .0100, .00000, -.0050] SUBUNIT[2, 5] = [ .0050, -.00866, -.0050] SUBUNIT[2, 6] = [-.0050, -.00866, -.0050] } SUBUNIT_RELATIONSHIPS { ring_negative = [ 0, -1] ring_positive = [ 0, +1] dimer_partner = [+1, 0] } RATE_RULES { coop_binding_rate { dimer_partner != camkii_subunit : fw_rate * TMP_spec_F DEFAULT : fw_rate } coop_unbinding_rate { dimer_partner != camkii_subunit : bw_rate * TMP_spec_B DEFAULT : bw_rate } } } DEFINE_REACTIONS { (camkii_subunit) + cam <-> (camkii_subunitB) [> COMPLEX_RATE camkii coop_bniding_rate, < COMPLEX_RATE camkii coop_unbinding_rate] } mainbox OBJECT { b BOX { CORNERS = [ -0.5, -0.5, -0.5 ], [ 0.5, 0.5, 0.5 ] } } INSTANTIATE world OBJECT { mainbox OBJECT mainbox { } rs1 RELEASE_SITE { SHAPE = world.mainbox.b[ALL] MOLECULE = camkii NUMBER_TO_RELEASE = num_complexes } rs2 RELEASE_SITE { SHAPE = world.mainbox.b[ALL] MOLECULE = cam NUMBER_TO_RELEASE = num_cam } } VIZ_OUTPUT { MODE = DREAMM_V3 FILENAME = "./viz_dat/test_box" MOLECULES { NAME_LIST { ALL_MOLECULES } ITERATION_NUMBERS { POSITIONS @ [[0 TO 100 STEP 10], [200 TO 1000 STEP 100], [2000 TO 100000 STEP 1000], [200000 TO iterations STEP 100000]] } } MESHES { NAME_LIST { ALL_MESHES } ITERATION_NUMBERS { ALL_DATA @ [0] } } } REACTION_DATA_OUTPUT { ITERATION_LIST = [[0 TO 9999 STEP 100], [10000 TO 250000 STEP 10000], [250001 TO 1250000 STEP 1]] {COUNT[SUBUNIT{camkii:camkii_subunit[dimer_partner==camkii_subunit]}, WORLD]} => "./reaction_data/coop_m00." & seed_str {COUNT[SUBUNIT{camkii:camkii_subunit[dimer_partner!=camkii_subunit]}, WORLD]} => "./reaction_data/coop_m01." & seed_str {COUNT[SUBUNIT{camkii:camkii_subunitB[dimer_partner==camkii_subunit]}, WORLD]} => "./reaction_data/coop_m10." & seed_str {COUNT[SUBUNIT{camkii:camkii_subunitB[dimer_partner!=camkii_subunit]}, WORLD]} => "./reaction_data/coop_m11." & seed_str {COUNT[cam, WORLD]} => "./reaction_data/coop_cam." & seed_str }