* Generation, minimization and dynamics of N-Acetyl-Histidine using the * asymmetric as the primary atoms. (protonated form imidazole)n * set id1 ace_hsp_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 read sequence card * hsp1 * 1 hsp generate hsp1 first ace last cter setup warn read sequence card * hsp2 * 1 hsp generate hsp2 first ace last cter setup warn join hsp1 hsp2 renumber ! Generate the three waters read sequence TIP3 2 generate wat setup warn NOANGLE NODIHEDRAL read coor card * L-N-Acetylhistidine monohydrate unit cell coordinates at Room Temp * Kistenmacher, T.J., Hunt, D.J. and Marsh R.E. * Acta Crystallography (1972) B28:3352-3361 * 56 1 1 HSP CAY 0.17370 0.41340 0.5042 HSP1 1 0.00000 2 1 HSP HY1 0.10500 0.33700 0.4070 HSP1 1 0.00000 3 1 HSP HY2 0.19000 0.53000 0.5070 HSP1 1 0.00000 4 1 HSP HY3 0.09700 0.38000 0.5900 HSP1 1 0.00000 5 1 HSP CY 0.33130 0.39790 0.54060 HSP1 1 0.00000 6 1 HSP OY 0.32860 0.25710 0.51370 HSP1 1 0.00000 7 1 HSP C 0.74560 0.70860 0.81910 HSP1 1 0.00000 8 1 HSP CA 0.63210 0.54500 0.66900 HSP1 1 0.00000 9 1 HSP HA 0.59500 0.45200 0.72500 HSP1 1 0.00000 10 1 HSP CB 0.73840 0.52810 0.50740 HSP1 1 0.00000 11 1 HSP HB1 0.66700 0.44400 0.39200 HSP1 1 0.00000 12 1 HSP HB2 0.82000 0.49300 0.54500 HSP1 1 0.00000 13 1 HSP CG 0.84290 0.69370 0.45300 HSP1 1 0.00000 14 1 HSP CE1 0.89880 0.91690 0.34090 HSP1 1 0.00000 15 1 HSP HE1 0.88200 0.98800 0.27600 HSP1 1 0.00000 16 1 HSP CD2 1.01070 0.81040 0.50520 HSP1 1 0.00000 17 1 HSP HD2 1.09700 0.80100 0.57600 HSP1 1 0.00000 18 1 HSP N 0.47620 0.54390 0.60630 HSP1 1 0.00000 19 1 HSP HN 0.46400 0.64300 0.62300 HSP1 1 0.00000 20 1 HSP ND1 0.77640 0.76410 0.35010 HSP1 1 0.00000 21 1 HSP HD1 0.66300 0.71900 0.29200 HSP1 1 0.00000 22 1 HSP NE2 1.04150 0.94820 0.43430 HSP1 1 0.00000 23 1 HSP HE2 1.14800 1.04400 0.45800 HSP1 1 0.00000 24 1 HSP OT1 0.86320 0.70550 0.91070 HSP1 1 0.00000 25 1 HSP OT2 0.71990 0.83290 0.83090 HSP1 1 0.00000 26 2 HSP CAY 0.65610 1.08950 1.57900 HSP1 2 0.00000 27 2 HSP HY1 0.70500 1.04200 1.65400 HSP1 2 0.00000 28 2 HSP HY2 0.73900 1.15800 1.50700 HSP1 2 0.00000 29 2 HSP HY3 0.61600 1.15300 1.66300 HSP1 2 0.00000 30 2 HSP CY 0.50050 0.93630 1.46260 HSP1 2 0.00000 31 2 HSP OY 0.38800 0.83250 1.53390 HSP1 2 0.00000 32 2 HSP C 0.33840 0.61200 1.10230 HSP1 2 0.00000 33 2 HSP CA 0.34430 0.78770 1.14930 HSP1 2 0.00000 34 2 HSP HA 0.24200 0.77300 1.20700 HSP1 2 0.00000 35 2 HSP CB 0.33950 0.84000 0.96590 HSP1 2 0.00000 36 2 HSP HB1 0.43700 0.85900 0.89900 HSP1 2 0.00000 37 2 HSP HB2 0.23800 0.74100 0.88400 HSP1 2 0.00000 38 2 HSP CG 0.32080 0.99810 0.98880 HSP1 2 0.00000 39 2 HSP CE1 0.18570 1.15020 1.00910 HSP1 2 0.00000 40 2 HSP HE1 0.09400 1.17800 1.00400 HSP1 2 0.00000 41 2 HSP CD2 0.43890 1.16570 1.01840 HSP1 2 0.00000 42 2 HSP HD2 0.56500 1.22500 1.02900 HSP1 2 0.00000 43 2 HSP N 0.49300 0.92080 1.27770 HSP1 2 0.00000 44 2 HSP HN 0.57900 0.99100 1.23400 HSP1 2 0.00000 45 2 HSP ND1 0.16310 0.99220 0.98450 HSP1 2 0.00000 46 2 HSP HD1 0.04600 0.88700 0.96000 HSP1 2 0.00000 47 2 HSP NE2 0.35120 1.25710 1.03020 HSP1 2 0.00000 48 2 HSP HE2 0.40200 1.37900 1.06000 HSP1 2 0.00000 49 2 HSP OT1 0.20000 0.48800 1.02000 HSP1 2 0.00000 50 2 HSP OT2 0.46940 0.59930 1.13940 HSP1 2 0.00000 51 3 TIP3 OH2 0.79940 0.12290 0.10360 WAT 3 0.00000 52 3 TIP3 H1 0.77800 0.03900 0.00800 WAT 3 0.00000 53 3 TIP3 H2 0.81600 0.20300 0.07000 WAT 3 0.00000 54 4 TIP3 OH2 0.86980 0.42410 1.00160 WAT 4 0.00000 55 4 TIP3 H1 0.99300 0.47100 1.02800 WAT 4 0.00000 56 4 TIP3 H2 0.85700 0.49900 0.98000 WAT 4 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 !FRACtional are often reported by crystallographers coor conv fractional symmetric - 8.865 9.097 7.346 102.24 90.30 117.73 ! define the crystal lattice type and geometry crystal define triclinic 8.865 9.097 7.346 102.24 90.30 117.73 ! 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 (RESID 1 .and. segid hsp1) .and. .not. (type c* .or. hydrogen) end - sele .not. (RESID 1 .and. segid hsp1) .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 (RESID 1 .and. segid hsp1) .and. .not. (type c* .or. hydrogen) end - sele .not. (RESID 1 .and. segid hsp1) .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