#============================================================* # test lennard-jones potential * # * # use ca and just repulsive part. * # * # specify a two lists of potentials. * #============================================================* 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 hc backbone color = [ 0.6 0.6 0.6 ] width = 2 show domain create iq1 = AC[760-788] domain iq1 backbone color = [ 1 0 0 ] width = 2 show domain create iq2 = BC[788-814] domain iq2 backbone color = [ 0 1 0 ] width = 2 show domain create iq3 = DC[814-836] domain iq3 backbone color = [ 1 0.6 0 ] width = 2 show domain create hcj = J domain hcj backbone color = [ 0.0 0.6 0.6 ] width = 2 show domain create iq4 = IJ[760-788] domain iq4 backbone color = [ 1 0 0.5 ] width = 2 show domain create iq5 = KJ[788-814] domain iq5 backbone color = [ 0 1 0.5 ] width = 2 show domain create iq6 = LJ[814-836] domain iq6 backbone color = [ 1 0.6 0.5 ] width = 2 show #--------------------------------------------------------------# # create bodies # #--------------------------------------------------------------# # 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 # 2nd group body create name = iq4_body type = rigid domain = iq4 body create name = iq5_body type = rigid domain = iq5 body create name = iq6_body type = rigid domain = iq6 #--------------------------------------------------------------# # create joints # #--------------------------------------------------------------# # 1st group joint create name = jnt1 type = ball domain = hc res = C[760] use = CA joint jnt1 bodies = { ground iq1_body } joint jnt1 color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint create name = jnt2 type = ball domain = hc res = C[788] use = CA joint jnt2 bodies = { iq1_body iq2_body } joint jnt2 color = [ 0 1 0 ] msize = 0.1 shading = color show = true joint create name = jnt3 type = ball domain = hc res = C[814] use = CA joint jnt3 bodies = { iq2_body iq3_body } joint jnt3 color = [ 0 0 1 ] msize = 0.1 shading = color show = true # 2nd group joint create name = jnt4 type = ball domain = hcj res = J[760] use = CA joint jnt4 bodies = { ground iq4_body } joint jnt4 color = [ 1 0 0 ] msize = 0.1 shading = color show = true joint create name = jnt5 type = ball domain = hcj res = J[788] use = CA joint jnt5 bodies = { iq4_body iq5_body } joint jnt5 color = [ 0 1 0 ] msize = 0.1 shading = color show = true joint create name = jnt6 type = ball domain = hcj res = J[814] use = CA joint jnt6 bodies = { iq5_body iq6_body } joint jnt6 color = [ 0 0 1 ] msize = 0.1 shading = color show = true #--------------------------------------------------------------# # create a rigid simulation # #--------------------------------------------------------------# simulation create name = rsim type = rigid # add bodies #----------- simulation rsim add body = ground simulation rsim add body = iq1_body simulation rsim add body = iq2_body simulation rsim add body = iq3_body simulation rsim add body = iq4_body simulation rsim add body = iq5_body simulation rsim add body = iq6_body # add joints #----------- simulation rsim add joint = jnt1 simulation rsim add joint = jnt2 simulation rsim add joint = jnt3 simulation rsim add joint = jnt4 simulation rsim add joint = jnt5 simulation rsim add joint = jnt6 # 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 = [ 4 -4 0 ] \ scale = 1.0 simulation rsim add force = force1 \ body = iq3_body \ time = { 0 10 } # add interaction potentials #--------------------------- variable show = true domain iq1 define region = iq1_rgn residues = A[1-148] atom_names = { CA } domain iq2 define region = iq2_rgn residues = B[1-148] atom_names = { CA } domain iq3 define region = iq3_rgn residues = D[1-148] atom_names = { CA } domain iq4 define region = iq4_rgn residues = I[1-148] atom_names = { CA } domain iq5 define region = iq5_rgn residues = K[1-148] atom_names = { CA } domain iq6 define region = iq6_rgn residues = L[1-148] atom_names = { CA } body iq1_body add potential = iq1_mm \ type = molecular-mechanics region = iq1_rgn geometry = points \ display_spheres = true display = solid color = [ 1 0 0 ] show = ${show} body iq2_body add potential = iq2_mm \ type = molecular-mechanics region = iq2_rgn geometry = points \ display_spheres = true display = solid color = [ 0 1 0 ] show = ${show} body iq3_body add potential = iq3_mm \ type = molecular-mechanics region = iq3_rgn geometry = points \ display_spheres = true display = solid color = [ 1 0.7 0 ] show = ${show} #----------# body iq4_body add potential = iq4_mm \ type = molecular-mechanics region = iq4_rgn geometry = points \ display_spheres = true display = solid color = [ 1 0 0.5 ] show = ${show} body iq5_body add potential = iq5_mm \ type = molecular-mechanics region = iq5_rgn geometry = points \ display_spheres = true color = [ 0 1 0.5 ] show = ${show} body iq6_body add potential = iq6_mm \ type = molecular-mechanics region = iq6_rgn geometry = points \ display_spheres = true color = [ 1 0.6 0.5 ] show = ${show} simulation rsim add interaction = mm1 \ list1 = { iq1_mm iq2_mm iq3_mm } \ list2 = { iq4_mm iq5_mm iq6_mm } \ time = { 0.0 10.0 } # initialize simulation #---------------------- simulation rsim initialize simulation rsim momentum = on simulation rsim time step = 0.005 simulation state save_frequency = 10 #simulation rsim write energy = true contact = true file_name = rsim graphics center point = [ 4.64212, 5.15401, 5.41185 ]