* Generation of imidazole crystal using the * full unitcell as the primary atoms * followed by trajectory analysis * !Analysis of dynamics trajectories should !be performed on individual time frames with !the data averaged over the simulations. Use !of dynamics averaged coordinates is not appropriate !as those coordinates do not correspond to any !real structure set id1 imi20_xtal_uc_1 ! output identifier !variables for analysis of trajectory set begin 50 set stop 1000 set skip 50 ! 1: topology ! 2: parameter ! 3: cutim ! 4: cutnb ! 5: ctonnb ! 6: ctofnb ! 7: electrostatic cutoff regime (shift or switch) ! 8: electrostatic pairing method (atom or group) ! 9: VDW pairing method (vatom or vgroup) ! VDW cutoff regime is vwsitch set a top_all22_model.inp set b par_all22_prot.inp ! note use of short nonbond lists to save CPU set 3 4.0 set 4 4.0 set 5 1.0 set 6 2.0 set 7 switch !associated with use of PMEwald set 8 atom set 9 vatom open unit 20 read card name @a read rtf card unit 20 close unit 20 open unit 20 read card name @b read para card unit 20 close unit 20 ! generate imidazole monomer read sequence card * imidazole * 4 imia imia imia imia generate imi1 setup read coor card * IMIDAZOLE 20 C FULL UNITCELL COORDINATES (4 IMIDAZOLES) * 20C, CRAVEN, B.M., MCMULLAN, R.K., BELL, J.D. AND FREEMAN, H.C. * 1977, ACTA CRYST. B33:2585-2589. * A=7.732,B=5.458,C=9.779,BETA=117.26 * DATE: 13/ 5/91 15:18:59 CREATED BY USER: * 36 1 1 IMIA CG 1.71876 2.93586 1.39869 IMI1 1 0.00000 2 1 IMIA HG 2.44554 3.59901 0.97708 IMI1 1 0.00000 3 1 IMIA CD2 1.05427 2.97625 2.58180 IMI1 1 0.00000 4 1 IMIA HD2 1.13098 3.70653 3.36329 IMI1 1 0.00000 5 1 IMIA ND1 1.29890 1.80332 0.76845 IMI1 1 0.00000 6 1 IMIA HD1 1.65221 1.44964 -0.14083 IMI1 1 0.00000 7 1 IMIA CE1 0.41566 1.20895 1.57776 IMI1 1 0.00000 8 1 IMIA HE1 -0.07455 0.27890 1.34219 IMI1 1 0.00000 9 1 IMIA NE2 0.23248 1.88847 2.68959 IMI1 1 0.00000 10 2 IMIA CG -0.52077 -0.20686 5.74515 C 1 1 0.00000 11 2 IMIA HG 0.20600 -0.87001 5.32354 C 1 1 0.00000 12 2 IMIA CD2 -1.18527 -0.24725 6.92825 C 1 1 0.00000 13 2 IMIA HD2 -1.10855 -0.97753 7.70975 C 1 1 0.00000 14 2 IMIA ND1 -0.94063 0.92568 5.11491 C 1 1 0.00000 15 2 IMIA HD1 -0.58732 1.27936 4.20563 C 1 1 0.00000 16 2 IMIA CE1 -1.82387 1.52005 5.92422 C 1 1 0.00000 17 2 IMIA HE1 -2.31409 2.45010 5.68864 C 1 1 0.00000 18 2 IMIA NE2 -2.00705 0.84053 7.03605 C 1 1 0.00000 19 3 IMIA CG -1.71876 -2.93586 -1.39869 C 2 1 0.00000 20 3 IMIA HG -2.44554 -3.59901 -0.97708 C 2 1 0.00000 21 3 IMIA CD2 -1.05427 -2.97625 -2.58180 C 2 1 0.00000 22 3 IMIA HD2 -1.13098 -3.70653 -3.36329 C 2 1 0.00000 23 3 IMIA ND1 -1.29890 -1.80332 -0.76845 C 2 1 0.00000 24 3 IMIA HD1 -1.65221 -1.44964 0.14083 C 2 1 0.00000 25 3 IMIA CE1 -0.41566 -1.20895 -1.57776 C 2 1 0.00000 26 3 IMIA HE1 0.07455 -0.27890 -1.34219 C 2 1 0.00000 27 3 IMIA NE2 -0.23248 -1.88847 -2.68959 C 2 1 0.00000 28 4 IMIA CG -3.95830 5.66486 2.94777 C 3 1 0.00000 29 4 IMIA HG -4.68507 6.32801 3.36937 C 3 1 0.00000 30 4 IMIA CD2 -3.29380 5.70525 1.76466 C 3 1 0.00000 31 4 IMIA HD2 -3.37052 6.43553 0.98317 C 3 1 0.00000 32 4 IMIA ND1 -3.53844 4.53232 3.57800 C 3 1 0.00000 33 4 IMIA HD1 -3.89174 4.17864 4.48728 C 3 1 0.00000 34 4 IMIA CE1 -2.65520 3.93795 2.76869 C 3 1 0.00000 35 4 IMIA HE1 -2.16498 3.00790 3.00427 C 3 1 0.00000 36 4 IMIA NE2 -2.47202 4.61747 1.65687 C 3 1 0.00000 !assign atom numbers to variable for quick commands !for first residue only ! coor stat sele ires 1 .and. type cg end set cg ?selatom coor stat sele ires 1 .and. type hg end set hg ?selatom coor stat sele ires 1 .and. type cd2 end set cd2 ?selatom coor stat sele ires 1 .and. type hd2 end set hd2 ?selatom coor stat sele ires 1 .and. type nd1 end set nd1 ?selatom coor stat sele ires 1 .and. type hd1 end set hd1 ?selatom coor stat sele ires 1 .and. type ce1 end set ce1 ?selatom coor stat sele ires 1 .and. type he1 end set he1 ?selatom coor stat sele ires 1 .and. type ne2 end set ne2 ?selatom !must work in SYMMETRIC coordinates with non-orthaganol crystal !(when one or more angles is not equal to 90 degrees !ALIGNed in the normal charmm standard coor conv aligned symmetric - 7.732 5.458 9.779 90.0 117.26 90.0 ! define the crystal lattice type and geometry crystal define monoclinic 7.732 5.458 9.779 90.0 117.26 90.0 ! build the crystal along with the images within the cutoff crystal build Noper 0 cutoff @3 !create nonbond list, note use of PMEwald update inbfrq -1 ihbfrq 0 imgfrq -1 - ewald spline kappa 0.31 pmewald order 6 fftx 8 ffty 8 fftz 8 - @7 @8 vswitch @9 cutim @3 cutnb @4 ctonnb @5 ctofnb @6 ! get initial IC's and some non-bond distances for comparison ic fill ic print ic fill comp coor dist cut 3.5 close image - sele ires 1 .and. .not. (type c* .or. hydrogen) end - sele .not. ires 1 .and. .not. (type c* .or. hydrogen) end !from xtal structure ! DISTANCES FOR SELECTED ATOMS ! 5 IMI1 IMIA 1 ND1 - 117 C006 IMIA 2 NE2 2.8610 ! 9 IMI1 IMIA 1 NE2 - 14 IMI1 IMIA 2 ND1 2.8610 !correl only works for primary to primary distances; must !set up a loop with coor dist to analyze primary to image !distances correl maxser 6 maxt 20000 inbfrq -1 ihbfrq 0 imgfrq -1 - ewald spline kappa 0.31 pmewald order 6 fftx 8 ffty 8 fftz 8 - @7 @8 vswitch @9 cutim @3 cutnb @4 ctonnb @5 ctofnb @6 !enter dis1 vect r imi1 1 nd1 C006 2 ne2 enter dis2 vect r imi1 1 ne2 imi1 2 nd1 set c 1 !number of trj units to open open read file unit 30 name dyn_@id1_0.trj trajectory firstu 30 nunit @c begin @begin stop @stop skip @skip end ! determine average internal coordinates and fluctuations ! via IC ! reopen trajectory open unit 30 read unform name dyn_@id1_0.trj ic dyna aver first 30 nunit @c nskip @skip begin @begin stop @stop ic print open unit 30 read unform name dyn_@id1_0.trj ic dyna fluc first 30 nunit @c nskip @skip begin @begin stop @stop ic print stop