* Generation, minimization and dynamics of L-Histidine using the * asymmetric as the primary atoms. * set id1 l_his_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 !loop to generate the 4 histidines set count 1 label gen_loop ! generate L-histidine unitcell read sequence card * l-histidine crystal * 1 hse generate his@count first nter last cter setup calc count = @count + 1 if count le 4 goto gen_loop read coor card * L-HISTIDINE FULL UNITCELL CARTESIAN COORDINATES * LEHMAN, M.S., KOETZLE, T.F. AND HAMILTON, W.C. * INT.J.PEPTIDE PROTEIN RES. (1972) 4:229-239 * DATE: 11/ 6/91 10: 3:52 CREATED BY USER: * 80 1 1 HSE N 2.13334 -1.30412 5.82188 HIS1 1 0.00000 2 1 HSE HT1 2.77251 -0.82118 5.16431 HIS1 1 0.00000 3 1 HSE HT2 2.60308 -1.34142 6.72412 HIS1 1 0.00000 4 1 HSE HT3 1.90921 -2.25317 5.48775 HIS1 1 0.00000 5 1 HSE CA 0.84798 -0.55053 5.98856 HIS1 1 0.00000 6 1 HSE HA 0.13714 -1.24084 6.46256 HIS1 1 0.00000 7 1 HSE NE2 1.93845 -0.00541 10.38713 HIS1 1 0.00000 8 1 HSE HE2 1.83376 -0.01009 11.42025 HIS1 1 0.00000 9 1 HSE CD2 1.07055 0.55631 9.47925 HIS1 1 0.00000 10 1 HSE HD2 0.20829 1.10442 9.76875 HIS1 1 0.00000 11 1 HSE ND1 2.76557 -0.43422 8.38406 HIS1 1 0.00000 12 1 HSE CG 1.60368 0.29019 8.24344 HIS1 1 0.00000 13 1 HSE CE1 2.91606 -0.60144 9.67331 HIS1 1 0.00000 14 1 HSE HE1 3.71989 -1.15409 10.12500 HIS1 1 0.00000 15 1 HSE CB 1.07666 0.65703 6.88575 HIS1 1 0.00000 16 1 HSE HB1 1.77979 1.35115 6.39225 HIS1 1 0.00000 17 1 HSE HB2 0.12063 1.16301 6.98981 HIS1 1 0.00000 18 1 HSE C 0.31578 -0.11426 4.62244 HIS1 1 0.00000 19 1 HSE OT1 1.16117 0.02867 3.71569 HIS1 1 0.00000 20 1 HSE OT2 -0.91794 0.06964 4.53919 HIS1 1 0.00000 21 2 HSE N 4.72084 4.96162 -5.82187 C 1 1 0.00000 22 2 HSE HT1 5.36001 4.47868 -5.16431 C 1 1 0.00000 23 2 HSE HT2 5.19058 4.99892 -6.72412 C 1 1 0.00000 24 2 HSE HT3 4.49671 5.91067 -5.48775 C 1 1 0.00000 25 2 HSE CA 3.43548 4.20803 -5.98856 C 1 1 0.00000 26 2 HSE HA 2.72464 4.89834 -6.46256 C 1 1 0.00000 27 2 HSE NE2 4.52595 3.66291 -10.38712 C 1 1 0.00000 28 2 HSE HE2 4.42126 3.66759 -11.42025 C 1 1 0.00000 29 2 HSE CD2 3.65805 3.10119 -9.47925 C 1 1 0.00000 30 2 HSE HD2 2.79579 2.55308 -9.76875 C 1 1 0.00000 31 2 HSE ND1 5.35307 4.09172 -8.38406 C 1 1 0.00000 32 2 HSE CG 4.19118 3.36731 -8.24344 C 1 1 0.00000 33 2 HSE CE1 5.50356 4.25894 -9.67331 C 1 1 0.00000 34 2 HSE HE1 6.30739 4.81159 -10.12500 C 1 1 0.00000 35 2 HSE CB 3.66416 3.00047 -6.88575 C 1 1 0.00000 36 2 HSE HB1 4.36729 2.30635 -6.39225 C 1 1 0.00000 37 2 HSE HB2 2.70813 2.49449 -6.98981 C 1 1 0.00000 38 2 HSE C 2.90328 3.77176 -4.62244 C 1 1 0.00000 39 2 HSE OT1 3.74867 3.62883 -3.71569 C 1 1 0.00000 40 2 HSE OT2 1.66956 3.58786 -4.53919 C 1 1 0.00000 41 3 HSE N -2.13334 2.35338 3.55313 C 2 1 0.00000 42 3 HSE HT1 -2.77251 2.83632 4.21069 C 2 1 0.00000 43 3 HSE HT2 -2.60308 2.31608 2.65088 C 2 1 0.00000 44 3 HSE HT3 -1.90921 1.40433 3.88725 C 2 1 0.00000 45 3 HSE CA -0.84798 3.10697 3.38644 C 2 1 0.00000 46 3 HSE HA -0.13714 2.41666 2.91244 C 2 1 0.00000 47 3 HSE NE2 -1.93845 3.65209 -1.01212 C 2 1 0.00000 48 3 HSE HE2 -1.83376 3.64741 -2.04525 C 2 1 0.00000 49 3 HSE CD2 -1.07055 4.21381 -0.10425 C 2 1 0.00000 50 3 HSE HD2 -0.20829 4.76192 -0.39375 C 2 1 0.00000 51 3 HSE ND1 -2.76557 3.22328 0.99094 C 2 1 0.00000 52 3 HSE CG -1.60368 3.94769 1.13156 C 2 1 0.00000 53 3 HSE CE1 -2.91606 3.05606 -0.29831 C 2 1 0.00000 54 3 HSE HE1 -3.71989 2.50341 -0.75000 C 2 1 0.00000 55 3 HSE CB -1.07666 4.31453 2.48925 C 2 1 0.00000 56 3 HSE HB1 -1.77979 5.00865 2.98275 C 2 1 0.00000 57 3 HSE HB2 -0.12063 4.82051 2.38519 C 2 1 0.00000 58 3 HSE C -0.31578 3.54324 4.75256 C 2 1 0.00000 59 3 HSE OT1 -1.16117 3.68617 5.65931 C 2 1 0.00000 60 3 HSE OT2 0.91794 3.72714 4.83581 C 2 1 0.00000 61 4 HSE N 0.45416 1.30412 15.19687 C 3 1 0.00000 62 4 HSE HT1 -0.18501 0.82118 14.53931 C 3 1 0.00000 63 4 HSE HT2 -0.01558 1.34142 16.09913 C 3 1 0.00000 64 4 HSE HT3 0.67829 2.25317 14.86275 C 3 1 0.00000 65 4 HSE CA 1.73952 0.55053 15.36356 C 3 1 0.00000 66 4 HSE HA 2.45036 1.24084 15.83756 C 3 1 0.00000 67 4 HSE NE2 0.64905 0.00541 19.76212 C 3 1 0.00000 68 4 HSE HE2 0.75374 0.01009 20.79525 C 3 1 0.00000 69 4 HSE CD2 1.51695 -0.55631 18.85425 C 3 1 0.00000 70 4 HSE HD2 2.37921 -1.10442 19.14375 C 3 1 0.00000 71 4 HSE ND1 -0.17807 0.43422 17.75906 C 3 1 0.00000 72 4 HSE CG 0.98382 -0.29019 17.61844 C 3 1 0.00000 73 4 HSE CE1 -0.32856 0.60144 19.04831 C 3 1 0.00000 74 4 HSE HE1 -1.13239 1.15409 19.50000 C 3 1 0.00000 75 4 HSE CB 1.51084 -0.65703 16.26075 C 3 1 0.00000 76 4 HSE HB1 0.80771 -1.35115 15.76725 C 3 1 0.00000 77 4 HSE HB2 2.46687 -1.16301 16.36481 C 3 1 0.00000 78 4 HSE C 2.27172 0.11426 13.99744 C 3 1 0.00000 79 4 HSE OT1 1.42633 -0.02867 13.09069 C 3 1 0.00000 80 4 HSE OT2 3.50544 -0.06964 13.91419 C 3 1 0.00000 !coor print !must work in SYMMETRIC coordinates with non-orthoganol crystal !(when one or more angles is not equal to 90 degrees !ALIGNed in the normal charmm standard ! !not required due to unitcell being orthorhombic ! !coor conv aligned symmetric - !5.175 7.315 18.75 90.0 90.0 90.0 ! define the crystal lattice type and geometry crystal define orthorhombic 5.175 7.315 18.75 90.0 90.0 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 16 - @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 0.29 pmewald order 6 fftx 8 ffty 8 fftz 16 - @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 his1 .and. .not. (type c* .or. hydrogen) end - sele .not. segid his1 .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 his1 .and. .not. (type c* .or. hydrogen) end - sele .not. segid his1 .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 298.0 finalt 298.0 - tbath 298.0 - pconst pref 1.0 pmass 100.0 pgamma 0.0 - hoover tmass 100.0 reft 298.0 - iunwrite 51 iuncrd 60 nsavcrd 50 stop