CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 11:11:26 | Available memory: 830.566 MB INPUT: Reading Input from file pt-analysis1.in [parm ../../../build/noWAt.topo.hmr] Reading '../../../build/noWAt.topo.hmr' as Amber Topology [trajin trig.nc] Reading 'trig.nc' as Amber NetCDF [reference ../../../../../../A-form.pdb [a-form]] Reading '../../../../../../A-form.pdb' as PDB Setting active reference for distance-based masks: 'A-form.pdb' [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] Reference mask: [:1,2&!@H*](43) RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted. [distance dist_sugar_ox :1@O2' :2@O4'] DISTANCE: :1@O2' to :2@O4', center of mass. [distance dist_N3-O5p :1@N3 :1@O5'] DISTANCE: :1@N3 to :1@O5', center of mass. [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3'] Output range is -180 to 180 degrees. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chin] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chin] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES: 0: 'trig.nc' is a NetCDF AMBER trajectory with replica temperatures, Parm noWAt.topo.hmr (Orthogonal box) (reading 9866 of 9866) Coordinate processing will occur on 9866 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (14 actions): 0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] Target mask: [:1,2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 1: [distance dist_sugar_ox :1@O2' :2@O4'] :1@O2' (1 atoms) to :2@O4' (1 atoms), imaged. 2: [distance dist_N3-O5p :1@N3 :1@O5'] :1@N3 (1 atoms) to :1@O5' (1 atoms), imaged. 3: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 4: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 5: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 6: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 8: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chin] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 9: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 10: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 11: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 12: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 13: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chin] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- trig.nc (1-9866, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 9866 frames and processed 9866 frames. TIME: Trajectory processing: 0.0828 s TIME: Avg. throughput= 119166.1030 frames / second. ACTION OUTPUT: DATASETS: 16 data sets: noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb' 67 atoms rms_2_aform "rms_2_aform" (double, rms), size is 9866 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 9866 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 9866 COM "COM" (double, distance), size is 9866 g1 "g1" (double, torsion(gamma)), size is 9866 d1 "d1" (double, torsion(delta)), size is 9866 e1 "e1" (double, torsion(epsilon)), size is 9866 z1 "z1" (double, torsion(zeta)), size is 9866 c1 "c1" (double, torsion(chin)), size is 9866 a2 "a2" (double, torsion(alpha)), size is 9866 b2 "b2" (double, torsion(beta)), size is 9866 g2 "g2" (double, torsion(gamma)), size is 9866 d2 "d2" (double, torsion(delta)), size is 9866 c2 "c2" (double, torsion(chin)), size is 9866 ---------- RUN END --------------------------------------------------- [avg rms_2_aform out avg-rmsd-all.dat] AVERAGE: Calculating average of 1 data sets. Writing results to avg-rmsd-all.dat [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Hist: rmsd-hist.dat: Set up for 1 dimensions using the following datasets: [ rms_2_aform ] norm: Sum over bins will be normalized to 1.0. [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Hist: COM-hist.dat: Set up for 1 dimensions using the following datasets: [ COM ] norm: Sum over bins will be normalized to 1.0. [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Hist: distO2O4-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Hist: distN3-O5p-hist.dat: Set up for 1 dimensions using the following datasets: [ dist_N3-O5p ] norm: Sum over bins will be normalized to 1.0. [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Hist: 2dhist_rms-dist.gnu: Set up for 2 dimensions using the following datasets: [ rms_2_aform dist_sugar_ox ] norm: Sum over bins will be normalized to 1.0. [hist g1,-180,180,1 out dihed_g1-hist.dat name gamma_1 norm] Hist: dihed_g1-hist.dat: Set up for 1 dimensions using the following datasets: [ g1 ] norm: Sum over bins will be normalized to 1.0. [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Hist: dihed_d1-hist.dat: Set up for 1 dimensions using the following datasets: [ d1 ] norm: Sum over bins will be normalized to 1.0. [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Hist: dihed_e1-hist.dat: Set up for 1 dimensions using the following datasets: [ e1 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Hist: dihed_z1-hist.dat: Set up for 1 dimensions using the following datasets: [ z1 ] norm: Sum over bins will be normalized to 1.0. [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Hist: dihed_c1-hist.dat: Set up for 1 dimensions using the following datasets: [ c1 ] norm: Sum over bins will be normalized to 1.0. [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Hist: dihed_a2-hist.dat: Set up for 1 dimensions using the following datasets: [ a2 ] norm: Sum over bins will be normalized to 1.0. [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Hist: dihed_b2-hist.dat: Set up for 1 dimensions using the following datasets: [ b2 ] norm: Sum over bins will be normalized to 1.0. [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Hist: dihed_g2-hist.dat: Set up for 1 dimensions using the following datasets: [ g2 ] norm: Sum over bins will be normalized to 1.0. [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Hist: dihed_d2-hist.dat: Set up for 1 dimensions using the following datasets: [ d2 ] norm: Sum over bins will be normalized to 1.0. [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Hist: dihed_c2-hist.dat: Set up for 1 dimensions using the following datasets: [ c2 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 16 analyses: 0: [avg rms_2_aform out avg-rmsd-all.dat] 1: [hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm] Calculating bins from min=0 max=5 step=0.1. Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 797 Coordinates out of bounds (-1) Warning: Frame 886 Coordinates out of bounds (-1) Warning: Frame 1624 Coordinates out of bounds (-1) Warning: Frame 1638 Coordinates out of bounds (-1) Warning: Frame 1639 Coordinates out of bounds (-1) Warning: Frame 1896 Coordinates out of bounds (-1) Warning: Frame 2162 Coordinates out of bounds (-1) Warning: Frame 2640 Coordinates out of bounds (-1) Warning: Frame 2642 Coordinates out of bounds (-1) Warning: Frame 2828 Coordinates out of bounds (-1) Warning: Frame 2921 Coordinates out of bounds (-1) Warning: Frame 3128 Coordinates out of bounds (-1) Warning: Frame 3129 Coordinates out of bounds (-1) Warning: Frame 3131 Coordinates out of bounds (-1) Warning: Frame 3327 Coordinates out of bounds (-1) Warning: Frame 3431 Coordinates out of bounds (-1) Warning: Frame 3435 Coordinates out of bounds (-1) Warning: Frame 3496 Coordinates out of bounds (-1) Warning: Frame 3743 Coordinates out of bounds (-1) Warning: Frame 4237 Coordinates out of bounds (-1) Warning: Frame 4272 Coordinates out of bounds (-1) Warning: Frame 5317 Coordinates out of bounds (-1) Warning: Frame 5318 Coordinates out of bounds (-1) Warning: Frame 5319 Coordinates out of bounds (-1) Warning: Frame 5323 Coordinates out of bounds (-1) Warning: Frame 5324 Coordinates out of bounds (-1) Warning: Frame 5331 Coordinates out of bounds (-1) Warning: Frame 5594 Coordinates out of bounds (-1) Warning: Frame 5982 Coordinates out of bounds (-1) Warning: Frame 5984 Coordinates out of bounds (-1) Warning: Frame 5985 Coordinates out of bounds (-1) Warning: Frame 6961 Coordinates out of bounds (-1) Warning: Frame 6970 Coordinates out of bounds (-1) Warning: Frame 7310 Coordinates out of bounds (-1) Warning: Frame 7516 Coordinates out of bounds (-1) Warning: Frame 8600 Coordinates out of bounds (-1) Warning: Frame 8619 Coordinates out of bounds (-1) Warning: Frame 8640 Coordinates out of bounds (-1) Warning: Frame 8667 Coordinates out of bounds (-1) Warning: Frame 8889 Coordinates out of bounds (-1) Warning: Frame 9021 Coordinates out of bounds (-1) Warning: Frame 9728 Coordinates out of bounds (-1) Warning: Frame 9729 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9823 2: [hist COM,0,10,0.1 out COM-hist.dat name CoM norm] Calculating bins from min=0 max=10 step=0.1. Dim COM: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 218 Coordinates out of bounds (-1) Warning: Frame 252 Coordinates out of bounds (-1) Warning: Frame 254 Coordinates out of bounds (-1) Warning: Frame 255 Coordinates out of bounds (-1) Warning: Frame 259 Coordinates out of bounds (-1) Warning: Frame 648 Coordinates out of bounds (-1) Warning: Frame 649 Coordinates out of bounds (-1) Warning: Frame 650 Coordinates out of bounds (-1) Warning: Frame 748 Coordinates out of bounds (-1) Warning: Frame 751 Coordinates out of bounds (-1) Warning: Frame 752 Coordinates out of bounds (-1) Warning: Frame 786 Coordinates out of bounds (-1) Warning: Frame 787 Coordinates out of bounds (-1) Warning: Frame 792 Coordinates out of bounds (-1) Warning: Frame 794 Coordinates out of bounds (-1) Warning: Frame 795 Coordinates out of bounds (-1) Warning: Frame 797 Coordinates out of bounds (-1) Warning: Frame 806 Coordinates out of bounds (-1) Warning: Frame 886 Coordinates out of bounds (-1) Warning: Frame 887 Coordinates out of bounds (-1) Warning: Frame 889 Coordinates out of bounds (-1) Warning: Frame 892 Coordinates out of bounds (-1) Warning: Frame 1276 Coordinates out of bounds (-1) Warning: Frame 1365 Coordinates out of bounds (-1) Warning: Frame 1366 Coordinates out of bounds (-1) Warning: Frame 1367 Coordinates out of bounds (-1) Warning: Frame 1368 Coordinates out of bounds (-1) Warning: Frame 1573 Coordinates out of bounds (-1) Warning: Frame 1624 Coordinates out of bounds (-1) Warning: Frame 1636 Coordinates out of bounds (-1) Warning: Frame 1638 Coordinates out of bounds (-1) Warning: Frame 1639 Coordinates out of bounds (-1) Warning: Frame 1722 Coordinates out of bounds (-1) Warning: Frame 1741 Coordinates out of bounds (-1) Warning: Frame 1743 Coordinates out of bounds (-1) Warning: Frame 1896 Coordinates out of bounds (-1) Warning: Frame 1897 Coordinates out of bounds (-1) Warning: Frame 1918 Coordinates out of bounds (-1) Warning: Frame 2005 Coordinates out of bounds (-1) Warning: Frame 2006 Coordinates out of bounds (-1) Warning: Frame 2007 Coordinates out of bounds (-1) Warning: Frame 2017 Coordinates out of bounds (-1) Warning: Frame 2039 Coordinates out of bounds (-1) Warning: Frame 2142 Coordinates out of bounds (-1) Warning: Frame 2143 Coordinates out of bounds (-1) Warning: Frame 2151 Coordinates out of bounds (-1) Warning: Frame 2153 Coordinates out of bounds (-1) Warning: Frame 2154 Coordinates out of bounds (-1) Warning: Frame 2157 Coordinates out of bounds (-1) Warning: Frame 2162 Coordinates out of bounds (-1) Warning: Frame 2163 Coordinates out of bounds (-1) Warning: Frame 2164 Coordinates out of bounds (-1) Warning: Frame 2207 Coordinates out of bounds (-1) Warning: Frame 2208 Coordinates out of bounds (-1) Warning: Frame 2209 Coordinates out of bounds (-1) Warning: Frame 2213 Coordinates out of bounds (-1) Warning: Frame 2215 Coordinates out of bounds (-1) Warning: Frame 2300 Coordinates out of bounds (-1) Warning: Frame 2301 Coordinates out of bounds (-1) Warning: Frame 2640 Coordinates out of bounds (-1) Warning: Frame 2641 Coordinates out of bounds (-1) Warning: Frame 2642 Coordinates out of bounds (-1) Warning: Frame 2644 Coordinates out of bounds (-1) Warning: Frame 2647 Coordinates out of bounds (-1) Warning: Frame 2649 Coordinates out of bounds (-1) Warning: Frame 2650 Coordinates out of bounds (-1) Warning: Frame 2653 Coordinates out of bounds (-1) Warning: Frame 2805 Coordinates out of bounds (-1) Warning: Frame 2821 Coordinates out of bounds (-1) Warning: Frame 2822 Coordinates out of bounds (-1) Warning: Frame 2824 Coordinates out of bounds (-1) Warning: Frame 2825 Coordinates out of bounds (-1) Warning: Frame 2828 Coordinates out of bounds (-1) Warning: Frame 2829 Coordinates out of bounds (-1) Warning: Frame 2833 Coordinates out of bounds (-1) Warning: Frame 2921 Coordinates out of bounds (-1) Warning: Frame 2929 Coordinates out of bounds (-1) Warning: Frame 3128 Coordinates out of bounds (-1) Warning: Frame 3129 Coordinates out of bounds (-1) Warning: Frame 3130 Coordinates out of bounds (-1) Warning: Frame 3131 Coordinates out of bounds (-1) Warning: Frame 3151 Coordinates out of bounds (-1) Warning: Frame 3152 Coordinates out of bounds (-1) Warning: Frame 3156 Coordinates out of bounds (-1) Warning: Frame 3160 Coordinates out of bounds (-1) Warning: Frame 3161 Coordinates out of bounds (-1) Warning: Frame 3204 Coordinates out of bounds (-1) Warning: Frame 3209 Coordinates out of bounds (-1) Warning: Frame 3312 Coordinates out of bounds (-1) Warning: Frame 3316 Coordinates out of bounds (-1) Warning: Frame 3317 Coordinates out of bounds (-1) Warning: Frame 3318 Coordinates out of bounds (-1) Warning: Frame 3327 Coordinates out of bounds (-1) Warning: Frame 3335 Coordinates out of bounds (-1) Warning: Frame 3428 Coordinates out of bounds (-1) Warning: Frame 3429 Coordinates out of bounds (-1) Warning: Frame 3431 Coordinates out of bounds (-1) Warning: Frame 3433 Coordinates out of bounds (-1) Warning: Frame 3434 Coordinates out of bounds (-1) Warning: Frame 3435 Coordinates out of bounds (-1) Warning: Frame 3496 Coordinates out of bounds (-1) Warning: Frame 3500 Coordinates out of bounds (-1) Warning: Frame 3502 Coordinates out of bounds (-1) Warning: Frame 3503 Coordinates out of bounds (-1) Warning: Frame 3504 Coordinates out of bounds (-1) Warning: Frame 3520 Coordinates out of bounds (-1) Warning: Frame 3521 Coordinates out of bounds (-1) Warning: Frame 3522 Coordinates out of bounds (-1) Warning: Frame 3523 Coordinates out of bounds (-1) Warning: Frame 3527 Coordinates out of bounds (-1) Warning: Frame 3528 Coordinates out of bounds (-1) Warning: Frame 3530 Coordinates out of bounds (-1) Warning: Frame 3536 Coordinates out of bounds (-1) Warning: Frame 3584 Coordinates out of bounds (-1) Warning: Frame 3733 Coordinates out of bounds (-1) Warning: Frame 3743 Coordinates out of bounds (-1) Warning: Frame 3745 Coordinates out of bounds (-1) Warning: Frame 3919 Coordinates out of bounds (-1) Warning: Frame 3926 Coordinates out of bounds (-1) Warning: Frame 3945 Coordinates out of bounds (-1) Warning: Frame 3948 Coordinates out of bounds (-1) Warning: Frame 3950 Coordinates out of bounds (-1) Warning: Frame 3961 Coordinates out of bounds (-1) Warning: Frame 3963 Coordinates out of bounds (-1) Warning: Frame 3966 Coordinates out of bounds (-1) Warning: Frame 3968 Coordinates out of bounds (-1) Warning: Frame 4077 Coordinates out of bounds (-1) Warning: Frame 4079 Coordinates out of bounds (-1) Warning: Frame 4080 Coordinates out of bounds (-1) Warning: Frame 4216 Coordinates out of bounds (-1) Warning: Frame 4217 Coordinates out of bounds (-1) Warning: Frame 4218 Coordinates out of bounds (-1) Warning: Frame 4219 Coordinates out of bounds (-1) Warning: Frame 4220 Coordinates out of bounds (-1) Warning: Frame 4221 Coordinates out of bounds (-1) Warning: Frame 4222 Coordinates out of bounds (-1) Warning: Frame 4223 Coordinates out of bounds (-1) Warning: Frame 4224 Coordinates out of bounds (-1) Warning: Frame 4227 Coordinates out of bounds (-1) Warning: Frame 4230 Coordinates out of bounds (-1) Warning: Frame 4231 Coordinates out of bounds (-1) Warning: Frame 4232 Coordinates out of bounds (-1) Warning: Frame 4233 Coordinates out of bounds (-1) Warning: Frame 4236 Coordinates out of bounds (-1) Warning: Frame 4237 Coordinates out of bounds (-1) Warning: Frame 4239 Coordinates out of bounds (-1) Warning: Frame 4244 Coordinates out of bounds (-1) Warning: Frame 4245 Coordinates out of bounds (-1) Warning: Frame 4261 Coordinates out of bounds (-1) Warning: Frame 4262 Coordinates out of bounds (-1) Warning: Frame 4263 Coordinates out of bounds (-1) Warning: Frame 4269 Coordinates out of bounds (-1) Warning: Frame 4272 Coordinates out of bounds (-1) Warning: Frame 4288 Coordinates out of bounds (-1) Warning: Frame 4293 Coordinates out of bounds (-1) Warning: Frame 4294 Coordinates out of bounds (-1) Warning: Frame 4295 Coordinates out of bounds (-1) Warning: Frame 4297 Coordinates out of bounds (-1) Warning: Frame 4460 Coordinates out of bounds (-1) Warning: Frame 4557 Coordinates out of bounds (-1) Warning: Frame 4566 Coordinates out of bounds (-1) Warning: Frame 4568 Coordinates out of bounds (-1) Warning: Frame 4570 Coordinates out of bounds (-1) Warning: Frame 4595 Coordinates out of bounds (-1) Warning: Frame 4596 Coordinates out of bounds (-1) Warning: Frame 4658 Coordinates out of bounds (-1) Warning: Frame 4659 Coordinates out of bounds (-1) Warning: Frame 4682 Coordinates out of bounds (-1) Warning: Frame 4734 Coordinates out of bounds (-1) Warning: Frame 4735 Coordinates out of bounds (-1) Warning: Frame 4736 Coordinates out of bounds (-1) Warning: Frame 4737 Coordinates out of bounds (-1) Warning: Frame 4738 Coordinates out of bounds (-1) Warning: Frame 4739 Coordinates out of bounds (-1) Warning: Frame 4889 Coordinates out of bounds (-1) Warning: Frame 4890 Coordinates out of bounds (-1) Warning: Frame 4891 Coordinates out of bounds (-1) Warning: Frame 4934 Coordinates out of bounds (-1) Warning: Frame 5081 Coordinates out of bounds (-1) Warning: Frame 5084 Coordinates out of bounds (-1) Warning: Frame 5088 Coordinates out of bounds (-1) Warning: Frame 5089 Coordinates out of bounds (-1) Warning: Frame 5090 Coordinates out of bounds (-1) Warning: Frame 5175 Coordinates out of bounds (-1) Warning: Frame 5179 Coordinates out of bounds (-1) Warning: Frame 5184 Coordinates out of bounds (-1) Warning: Frame 5185 Coordinates out of bounds (-1) Warning: Frame 5317 Coordinates out of bounds (-1) Warning: Frame 5318 Coordinates out of bounds (-1) Warning: Frame 5319 Coordinates out of bounds (-1) Warning: Frame 5323 Coordinates out of bounds (-1) Warning: Frame 5324 Coordinates out of bounds (-1) Warning: Frame 5331 Coordinates out of bounds (-1) Warning: Frame 5447 Coordinates out of bounds (-1) Warning: Frame 5450 Coordinates out of bounds (-1) Warning: Frame 5452 Coordinates out of bounds (-1) Warning: Frame 5454 Coordinates out of bounds (-1) Warning: Frame 5455 Coordinates out of bounds (-1) Warning: Frame 5509 Coordinates out of bounds (-1) Warning: Frame 5510 Coordinates out of bounds (-1) Warning: Frame 5564 Coordinates out of bounds (-1) Warning: Frame 5594 Coordinates out of bounds (-1) Warning: Frame 5734 Coordinates out of bounds (-1) Warning: Frame 5735 Coordinates out of bounds (-1) Warning: Frame 5755 Coordinates out of bounds (-1) Warning: Frame 5757 Coordinates out of bounds (-1) Warning: Frame 5758 Coordinates out of bounds (-1) Warning: Frame 5825 Coordinates out of bounds (-1) Warning: Frame 5826 Coordinates out of bounds (-1) Warning: Frame 5827 Coordinates out of bounds (-1) Warning: Frame 5831 Coordinates out of bounds (-1) Warning: Frame 5832 Coordinates out of bounds (-1) Warning: Frame 5836 Coordinates out of bounds (-1) Warning: Frame 5850 Coordinates out of bounds (-1) Warning: Frame 5851 Coordinates out of bounds (-1) Warning: Frame 5852 Coordinates out of bounds (-1) Warning: Frame 5855 Coordinates out of bounds (-1) Warning: Frame 5856 Coordinates out of bounds (-1) Warning: Frame 5857 Coordinates out of bounds (-1) Warning: Frame 5865 Coordinates out of bounds (-1) Warning: Frame 5866 Coordinates out of bounds (-1) Warning: Frame 5869 Coordinates out of bounds (-1) Warning: Frame 5870 Coordinates out of bounds (-1) Warning: Frame 5871 Coordinates out of bounds (-1) Warning: Frame 5971 Coordinates out of bounds (-1) Warning: Frame 5982 Coordinates out of bounds (-1) Warning: Frame 5983 Coordinates out of bounds (-1) Warning: Frame 5984 Coordinates out of bounds (-1) Warning: Frame 5985 Coordinates out of bounds (-1) Warning: Frame 6117 Coordinates out of bounds (-1) Warning: Frame 6152 Coordinates out of bounds (-1) Warning: Frame 6153 Coordinates out of bounds (-1) Warning: Frame 6154 Coordinates out of bounds (-1) Warning: Frame 6222 Coordinates out of bounds (-1) Warning: Frame 6223 Coordinates out of bounds (-1) Warning: Frame 6687 Coordinates out of bounds (-1) Warning: Frame 6689 Coordinates out of bounds (-1) Warning: Frame 6690 Coordinates out of bounds (-1) Warning: Frame 6691 Coordinates out of bounds (-1) Warning: Frame 6696 Coordinates out of bounds (-1) Warning: Frame 6698 Coordinates out of bounds (-1) Warning: Frame 6743 Coordinates out of bounds (-1) Warning: Frame 6744 Coordinates out of bounds (-1) Warning: Frame 6807 Coordinates out of bounds (-1) Warning: Frame 6855 Coordinates out of bounds (-1) Warning: Frame 6891 Coordinates out of bounds (-1) Warning: Frame 6892 Coordinates out of bounds (-1) Warning: Frame 6894 Coordinates out of bounds (-1) Warning: Frame 6895 Coordinates out of bounds (-1) Warning: Frame 6900 Coordinates out of bounds (-1) Warning: Frame 6902 Coordinates out of bounds (-1) Warning: Frame 6904 Coordinates out of bounds (-1) Warning: Frame 6905 Coordinates out of bounds (-1) Warning: Frame 6907 Coordinates out of bounds (-1) Warning: 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bounds (-1) Warning: Frame 7424 Coordinates out of bounds (-1) Warning: Frame 7503 Coordinates out of bounds (-1) Warning: Frame 7505 Coordinates out of bounds (-1) Warning: Frame 7512 Coordinates out of bounds (-1) Warning: Frame 7516 Coordinates out of bounds (-1) Warning: Frame 7521 Coordinates out of bounds (-1) Warning: Frame 7523 Coordinates out of bounds (-1) Warning: Frame 7615 Coordinates out of bounds (-1) Warning: Frame 7778 Coordinates out of bounds (-1) Warning: Frame 7780 Coordinates out of bounds (-1) Warning: Frame 7781 Coordinates out of bounds (-1) Warning: Frame 7782 Coordinates out of bounds (-1) Warning: Frame 7783 Coordinates out of bounds (-1) Warning: Frame 7784 Coordinates out of bounds (-1) Warning: Frame 7787 Coordinates out of bounds (-1) Warning: Frame 7789 Coordinates out of bounds (-1) Warning: Frame 7790 Coordinates out of bounds (-1) Warning: Frame 7800 Coordinates out of bounds (-1) Warning: Frame 7801 Coordinates out of bounds (-1) Warning: Frame 7802 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Warning: Frame 8154 Coordinates out of bounds (-1) Warning: Frame 8156 Coordinates out of bounds (-1) Warning: Frame 8158 Coordinates out of bounds (-1) Warning: Frame 8353 Coordinates out of bounds (-1) Warning: Frame 8354 Coordinates out of bounds (-1) Warning: Frame 8355 Coordinates out of bounds (-1) Warning: Frame 8356 Coordinates out of bounds (-1) Warning: Frame 8357 Coordinates out of bounds (-1) Warning: Frame 8382 Coordinates out of bounds (-1) Warning: Frame 8395 Coordinates out of bounds (-1) Warning: Frame 8396 Coordinates out of bounds (-1) Warning: Frame 8397 Coordinates out of bounds (-1) Warning: Frame 8398 Coordinates out of bounds (-1) Warning: Frame 8401 Coordinates out of bounds (-1) Warning: Frame 8409 Coordinates out of bounds (-1) Warning: Frame 8410 Coordinates out of bounds (-1) Warning: Frame 8489 Coordinates out of bounds (-1) Warning: Frame 8490 Coordinates out of bounds (-1) Warning: Frame 8492 Coordinates out of bounds (-1) Warning: Frame 8589 Coordinates out of bounds (-1) Warning: Frame 8597 Coordinates out of bounds (-1) Warning: Frame 8600 Coordinates out of bounds (-1) Warning: Frame 8615 Coordinates out of bounds (-1) Warning: Frame 8616 Coordinates out of bounds (-1) Warning: Frame 8617 Coordinates out of bounds (-1) Warning: Frame 8618 Coordinates out of bounds (-1) Warning: Frame 8619 Coordinates out of bounds (-1) Warning: Frame 8640 Coordinates out of bounds (-1) Warning: Frame 8667 Coordinates out of bounds (-1) Warning: Frame 8672 Coordinates out of bounds (-1) Warning: Frame 8673 Coordinates out of bounds (-1) Warning: Frame 8695 Coordinates out of bounds (-1) Warning: Frame 8705 Coordinates out of bounds (-1) Warning: Frame 8741 Coordinates out of bounds (-1) Warning: Frame 8742 Coordinates out of bounds (-1) Warning: Frame 8743 Coordinates out of bounds (-1) Warning: Frame 8744 Coordinates out of bounds (-1) Warning: Frame 8745 Coordinates out of bounds (-1) Warning: Frame 8746 Coordinates out of bounds (-1) Warning: Frame 8752 Coordinates out of bounds (-1) Warning: Frame 8786 Coordinates out of bounds (-1) Warning: Frame 8787 Coordinates out of bounds (-1) Warning: Frame 8889 Coordinates out of bounds (-1) Warning: Frame 8890 Coordinates out of bounds (-1) Warning: Frame 8892 Coordinates out of bounds (-1) Warning: Frame 8893 Coordinates out of bounds (-1) Warning: Frame 8894 Coordinates out of bounds (-1) Warning: Frame 8999 Coordinates out of bounds (-1) Warning: Frame 9017 Coordinates out of bounds (-1) Warning: Frame 9018 Coordinates out of bounds (-1) Warning: Frame 9019 Coordinates out of bounds (-1) Warning: Frame 9020 Coordinates out of bounds (-1) Warning: Frame 9021 Coordinates out of bounds (-1) Warning: Frame 9098 Coordinates out of bounds (-1) Warning: Frame 9099 Coordinates out of bounds (-1) Warning: Frame 9100 Coordinates out of bounds (-1) Warning: Frame 9102 Coordinates out of bounds (-1) Warning: Frame 9105 Coordinates out of bounds (-1) Warning: Frame 9111 Coordinates out of bounds (-1) Warning: Frame 9112 Coordinates out of bounds (-1) Warning: Frame 9334 Coordinates out of bounds (-1) Warning: Frame 9339 Coordinates out of bounds (-1) Warning: Frame 9341 Coordinates out of bounds (-1) Warning: Frame 9342 Coordinates out of bounds (-1) Warning: Frame 9343 Coordinates out of bounds (-1) Warning: Frame 9405 Coordinates out of bounds (-1) Warning: Frame 9453 Coordinates out of bounds (-1) Warning: Frame 9482 Coordinates out of bounds (-1) Warning: Frame 9498 Coordinates out of bounds (-1) Warning: Frame 9499 Coordinates out of bounds (-1) Warning: Frame 9500 Coordinates out of bounds (-1) Warning: Frame 9575 Coordinates out of bounds (-1) Warning: Frame 9576 Coordinates out of bounds (-1) Warning: Frame 9578 Coordinates out of bounds (-1) Warning: Frame 9579 Coordinates out of bounds (-1) Warning: Frame 9580 Coordinates out of bounds (-1) Warning: Frame 9581 Coordinates out of bounds (-1) Warning: Frame 9624 Coordinates out of bounds (-1) Warning: Frame 9625 Coordinates out of bounds (-1) Warning: Frame 9728 Coordinates out of bounds (-1) Warning: Frame 9729 Coordinates out of bounds (-1) Warning: Frame 9759 Coordinates out of bounds (-1) Warning: Frame 9783 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9470 3: [hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm] Calculating bins from min=0 max=10 step=0.1. Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 100 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 4: [hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm] Calculating bins from min=0 max=10 step=0.1. Dim dist_N3-O5p: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 100 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 5: [hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm] Calculating bins from min=0 max=5 step=0.1. Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Calculating bins from min=0 max=10 step=0.1. Dim dist_sugar_ox: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 5000 Warning: Frame 797 Coordinates out of bounds (-1) Warning: Frame 886 Coordinates out of bounds (-1) Warning: Frame 1624 Coordinates out of bounds (-1) Warning: Frame 1638 Coordinates out of bounds (-1) Warning: Frame 1639 Coordinates out of bounds (-1) Warning: Frame 1896 Coordinates out of bounds (-1) Warning: Frame 2162 Coordinates out of bounds (-1) Warning: Frame 2640 Coordinates out of bounds (-1) Warning: Frame 2642 Coordinates out of bounds (-1) Warning: Frame 2828 Coordinates out of bounds (-1) Warning: Frame 2921 Coordinates out of bounds (-1) Warning: Frame 3128 Coordinates out of bounds (-1) Warning: Frame 3129 Coordinates out of bounds (-1) Warning: Frame 3131 Coordinates out of bounds (-1) Warning: Frame 3327 Coordinates out of bounds (-1) Warning: Frame 3431 Coordinates out of bounds (-1) Warning: Frame 3435 Coordinates out of bounds (-1) Warning: Frame 3496 Coordinates out of bounds (-1) Warning: Frame 3743 Coordinates out of bounds (-1) Warning: Frame 4237 Coordinates out of bounds (-1) Warning: Frame 4272 Coordinates out of bounds (-1) Warning: Frame 5317 Coordinates out of bounds (-1) Warning: Frame 5318 Coordinates out of bounds (-1) Warning: Frame 5319 Coordinates out of bounds (-1) Warning: Frame 5323 Coordinates out of bounds (-1) Warning: Frame 5324 Coordinates out of bounds (-1) Warning: Frame 5331 Coordinates out of bounds (-1) Warning: Frame 5594 Coordinates out of bounds (-1) Warning: Frame 5982 Coordinates out of bounds (-1) Warning: Frame 5984 Coordinates out of bounds (-1) Warning: Frame 5985 Coordinates out of bounds (-1) Warning: Frame 6961 Coordinates out of bounds (-1) Warning: Frame 6970 Coordinates out of bounds (-1) Warning: Frame 7310 Coordinates out of bounds (-1) Warning: Frame 7516 Coordinates out of bounds (-1) Warning: Frame 8600 Coordinates out of bounds (-1) Warning: Frame 8619 Coordinates out of bounds (-1) Warning: Frame 8640 Coordinates out of bounds (-1) Warning: Frame 8667 Coordinates out of bounds (-1) Warning: Frame 8889 Coordinates out of bounds (-1) Warning: Frame 9021 Coordinates out of bounds (-1) Warning: Frame 9728 Coordinates out of bounds (-1) Warning: Frame 9729 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9823 6: [hist g1,-180,180,1 out dihed_g1-hist.dat name gamma_1 norm] Calculating bins from min=-180 max=180 step=1. Dim g1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 7: [hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm] Calculating bins from min=-180 max=180 step=1. Dim d1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 8: [hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm] Calculating bins from min=-180 max=180 step=1. Dim e1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 9: [hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm] Calculating bins from min=-180 max=180 step=1. Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 10: [hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm] Calculating bins from min=-180 max=180 step=1. Dim c1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 11: [hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm] Calculating bins from min=-180 max=180 step=1. Dim a2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 12: [hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm] Calculating bins from min=-180 max=180 step=1. Dim b2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 13: [hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm] Calculating bins from min=-180 max=180 step=1. Dim g2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 14: [hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm] Calculating bins from min=-180 max=180 step=1. Dim d2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 15: [hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm] Calculating bins from min=-180 max=180 step=1. Dim c2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 9866 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 9866 TIME: Analyses took 0.0030 seconds. DATASETS: 31 data sets: noWAt.topo.hmr "noWAt.topo.hmr" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../../A-form.pdb' 67 atoms rms_2_aform "rms_2_aform" (double, rms), size is 9866 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 9866 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 9866 COM "COM" (double, distance), size is 9866 g1 "g1" (double, torsion(gamma)), size is 9866 d1 "d1" (double, torsion(delta)), size is 9866 e1 "e1" (double, torsion(epsilon)), size is 9866 z1 "z1" (double, torsion(zeta)), size is 9866 c1 "c1" (double, torsion(chin)), size is 9866 a2 "a2" (double, torsion(alpha)), size is 9866 b2 "b2" (double, torsion(beta)), size is 9866 g2 "g2" (double, torsion(gamma)), size is 9866 d2 "d2" (double, torsion(delta)), size is 9866 c2 "c2" (double, torsion(chin)), size is 9866 RMSD "RMSD" (double), size is 50 CoM "CoM" (double), size is 100 Hist_00018 "Hist_00018" (double), size is 100 Hist_00019 "Hist_00019" (double), size is 100 Hist_00020 "Hist_00020" (double matrix), size is 5000 gamma_1 "gamma_1" (double), size is 360 delta_1 "delta_1" (double), size is 360 epsilon_1 "epsilon_1" (double), size is 360 zeta_1 "zeta_1" (double), size is 360 chi_1 "chi_1" (double), size is 360 alpha_2 "alpha_2" (double), size is 360 beta_2 "beta_2" (double), size is 360 gamma_2 "gamma_2" (double), size is 360 delta_2 "delta_2" (double), size is 360 chi_2 "chi_2" (double), size is 360 DATAFILES: rmsd-hist.dat (Standard Data File): RMSD COM-hist.dat (Standard Data File): CoM distO2O4-hist.dat (Standard Data File): Hist_00018 distN3-O5p-hist.dat (Standard Data File): Hist_00019 2dhist_rms-dist.gnu (Gnuplot File): Hist_00020 dihed_g1-hist.dat (Standard Data File): gamma_1 dihed_d1-hist.dat (Standard Data File): delta_1 dihed_e1-hist.dat (Standard Data File): epsilon_1 dihed_z1-hist.dat (Standard Data File): zeta_1 dihed_c1-hist.dat (Standard Data File): chi_1 dihed_a2-hist.dat (Standard Data File): alpha_2 dihed_b2-hist.dat (Standard Data File): beta_2 dihed_g2-hist.dat (Standard Data File): gamma_2 dihed_d2-hist.dat (Standard Data File): delta_2 dihed_c2-hist.dat (Standard Data File): chi_2 avg-rmsd-all.dat (DataSet Average) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.1235 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.