* Generation and minimization of imidazole crystal using the * full unitcell as the primary atoms. * set id1 imi20_xtal_uc_1 ! output identifier ! 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 set 3 14.0 set 4 14.0 set 5 10.0 set 6 12.0 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 !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 !skip over kappa test if already performed goto skip_pme_test !loop to determine best value of kappa set kappa 0.2 open unit 90 write form name @id1_kappa.ene label loop energy inbfrq -1 ihbfrq 0 imgfrq -1 - ewald spline kappa @kappa pmewald order 6 fftx 8 ffty 8 fftz 8 - @7 @8 vswitch @9 cutim @3 cutnb @4 ctonnb @5 ctofnb @6 write title unit 90 * @kappa ?ener ?elec ?ewks ?ewse * calc kappa = @kappa + 0.01 if kappa le 0.4 goto loop stop label skip_pme_test !create nonbond list, note use of PMEwald !kappa determined via above loop ! 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 !turn on SHAKE of all covalent bonds involving hydrogen SHAKE bonh param ! 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 segid imi1 .and. .not. (type c* .or. hydrogen) end - sele .not. segid imi1 .and. .not. (type c* .or. hydrogen) end coor copy comp ! initial minimization with lattice parameters held constant ! and heavy atoms harmonically constrained cons harm force 5.0 sele .not. hydrogen show end mini abnr nstep 50 nprint 10 tolstp 0.000001 - tolgrd 0.000001 tolenr 0.000001 pstr 0.00000001 ! lattice cons harm clear ! additional minimization with lattice parameters held constant mini abnr nstep 200 nprint 20 tolstp 0.000001 - tolgrd 0.000001 tolenr 0.000001 pstr 0.00000001 ! lattice ! continued minimization, including lattice parameters ! initial minimization with lattice parameters held constant mini abnr nstep 200 nprint 20 tolstp 0.000000001 - tolgrd 0.01 tolenr 0.000000001 pstr 0.000000001 lattice !obtain info on geometries and nonbonded distances ic fill ic print ic diff ic print coor dist cut 3.5 close image - sele segid imi1 .and. .not. (type c* .or. hydrogen) end - sele .not. segid imi1 .and. .not. (type c* .or. hydrogen) end !perform NPT dynamics !temperature should correspond to that at !which the experiments were performed open write card unit 51 name dyn_@id1_0.rst open write file unit 60 name dyn_@id1_0.trj DYNA cpt strt nstep 1000 time 0.002 ntrfrq 50 - iprfrq 50 nprint 50 - iasvel 1 firstt 293.0 finalt 293.0 - tbath 293.0 - pconst pref 1.0 pmass 100.0 pgamma 0.0 - hoover tmass 100.0 reft 293.0 - iunwrite 51 iuncrd 60 nsavcrd 50 stop