CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 11:01:16 | Available memory: 724.078 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, 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@N1 :1@C2 type chin] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2] 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@N1 :2@C2 type chin] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2] 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 12560 of 12560) Coordinate processing will occur on 12560 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (6 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (6 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@N1 :1@C2 type chin] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](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@N1 :2@C2 type chin] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- trig.nc (1-12560, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 12560 frames and processed 12560 frames. TIME: Trajectory processing: 0.1333 s TIME: Avg. throughput= 94217.9014 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 12560 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 12560 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 12560 COM "COM" (double, distance), size is 12560 g1 "g1" (double, torsion(gamma)), size is 12560 d1 "d1" (double, torsion(delta)), size is 12560 e1 "e1" (double, torsion(epsilon)), size is 12560 z1 "z1" (double, torsion(zeta)), size is 12560 c1 "c1" (double, torsion(chin)), size is 12560 a2 "a2" (double, torsion(alpha)), size is 12560 b2 "b2" (double, torsion(beta)), size is 12560 g2 "g2" (double, torsion(gamma)), size is 12560 d2 "d2" (double, torsion(delta)), size is 12560 c2 "c2" (double, torsion(chin)), size is 12560 ---------- 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: 12560 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 205 Coordinates out of bounds (-1) Warning: Frame 206 Coordinates out of bounds (-1) Warning: Frame 2573 Coordinates out of bounds (-1) Warning: Frame 3190 Coordinates out of bounds (-1) Warning: Frame 3192 Coordinates out of bounds (-1) Warning: Frame 3506 Coordinates out of bounds (-1) Warning: Frame 4695 Coordinates out of bounds (-1) Warning: Frame 4863 Coordinates out of bounds (-1) Warning: Frame 5713 Coordinates out of bounds (-1) Warning: Frame 5714 Coordinates out of bounds (-1) Warning: Frame 6130 Coordinates out of bounds (-1) Warning: Frame 6294 Coordinates out of bounds (-1) Warning: Frame 6541 Coordinates out of bounds (-1) Warning: Frame 7618 Coordinates out of bounds (-1) Warning: Frame 7619 Coordinates out of bounds (-1) Warning: Frame 7844 Coordinates out of bounds (-1) Warning: Frame 7845 Coordinates out of bounds (-1) Warning: Frame 8209 Coordinates out of bounds (-1) Warning: Frame 8211 Coordinates out of bounds (-1) Warning: Frame 8284 Coordinates out of bounds (-1) Warning: Frame 8385 Coordinates out of bounds (-1) Warning: Frame 8386 Coordinates out of bounds (-1) Warning: Frame 8563 Coordinates out of bounds (-1) Warning: Frame 8565 Coordinates out of bounds (-1) Warning: Frame 9114 Coordinates out of bounds (-1) Warning: Frame 9194 Coordinates out of bounds (-1) Warning: Frame 9195 Coordinates out of bounds (-1) Warning: Frame 9278 Coordinates out of bounds (-1) Warning: Frame 9280 Coordinates out of bounds (-1) Warning: Frame 9295 Coordinates out of bounds (-1) Warning: Frame 9672 Coordinates out of bounds (-1) Warning: Frame 9835 Coordinates out of bounds (-1) Warning: Frame 10153 Coordinates out of bounds (-1) Warning: Frame 10352 Coordinates out of bounds (-1) Warning: Frame 11042 Coordinates out of bounds (-1) Warning: Frame 11672 Coordinates out of bounds (-1) Warning: Frame 11674 Coordinates out of bounds (-1) Warning: Frame 11675 Coordinates out of bounds (-1) Warning: Frame 11681 Coordinates out of bounds (-1) Warning: Frame 11683 Coordinates out of bounds (-1) Warning: Frame 12227 Coordinates out of bounds (-1) Warning: Frame 12229 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 12518 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: 12560 data points in each dimension. Hist: Allocating histogram, total bins = 100 Warning: Frame 26 Coordinates out of bounds (-1) Warning: Frame 205 Coordinates out of bounds (-1) Warning: Frame 206 Coordinates out of bounds (-1) Warning: Frame 220 Coordinates out of bounds (-1) Warning: Frame 222 Coordinates out of bounds (-1) Warning: Frame 224 Coordinates out of bounds (-1) Warning: Frame 225 Coordinates out of bounds (-1) Warning: Frame 226 Coordinates out of bounds (-1) Warning: Frame 227 Coordinates out of bounds (-1) Warning: Frame 228 Coordinates out of bounds (-1) Warning: Frame 229 Coordinates out of bounds (-1) Warning: Frame 230 Coordinates out of bounds (-1) Warning: Frame 231 Coordinates out of bounds (-1) Warning: Frame 243 Coordinates out of bounds (-1) Warning: Frame 244 Coordinates out of bounds (-1) Warning: Frame 250 Coordinates out of bounds (-1) Warning: Frame 251 Coordinates out of bounds (-1) Warning: Frame 260 Coordinates out of bounds (-1) Warning: Frame 265 Coordinates out of bounds (-1) Warning: Frame 267 Coordinates out of bounds (-1) Warning: Frame 269 Coordinates out of bounds (-1) Warning: Frame 294 Coordinates out of bounds (-1) Warning: Frame 295 Coordinates out of bounds (-1) Warning: Frame 363 Coordinates out of bounds (-1) Warning: Frame 379 Coordinates out of bounds (-1) Warning: Frame 436 Coordinates out of bounds (-1) Warning: Frame 437 Coordinates out of bounds (-1) Warning: Frame 524 Coordinates out of bounds (-1) Warning: Frame 529 Coordinates out of bounds (-1) Warning: Frame 559 Coordinates out of bounds (-1) Warning: Frame 560 Coordinates out of bounds (-1) Warning: Frame 681 Coordinates out of bounds (-1) Warning: Frame 870 Coordinates out of bounds (-1) Warning: Frame 873 Coordinates out of bounds (-1) Warning: Frame 877 Coordinates out of bounds (-1) Warning: Frame 879 Coordinates out of bounds (-1) Warning: Frame 881 Coordinates out of bounds (-1) Warning: Frame 884 Coordinates out of bounds (-1) Warning: Frame 904 Coordinates out of bounds (-1) Warning: Frame 1133 Coordinates out of bounds (-1) Warning: Frame 1134 Coordinates out of bounds (-1) Warning: Frame 1135 Coordinates out of bounds (-1) Warning: Frame 1136 Coordinates out of bounds (-1) Warning: Frame 1193 Coordinates out of bounds (-1) Warning: Frame 1254 Coordinates out of bounds (-1) Warning: Frame 1257 Coordinates out of bounds (-1) Warning: Frame 1319 Coordinates out of bounds (-1) Warning: Frame 1325 Coordinates out of bounds (-1) Warning: Frame 1344 Coordinates out of bounds (-1) Warning: Frame 1366 Coordinates out of bounds (-1) Warning: Frame 1384 Coordinates out of bounds (-1) Warning: Frame 1390 Coordinates out of bounds (-1) Warning: Frame 1453 Coordinates out of bounds (-1) Warning: Frame 1454 Coordinates out of bounds (-1) Warning: Frame 1480 Coordinates out of bounds (-1) Warning: Frame 1481 Coordinates out of bounds (-1) Warning: Frame 1483 Coordinates out of bounds (-1) Warning: Frame 1484 Coordinates out of bounds (-1) Warning: Frame 1489 Coordinates out of bounds (-1) Warning: Frame 1501 Coordinates out of bounds (-1) Warning: Frame 1562 Coordinates out of bounds (-1) Warning: Frame 1563 Coordinates out of bounds (-1) Warning: Frame 1564 Coordinates out of bounds (-1) Warning: Frame 1565 Coordinates out of bounds (-1) Warning: Frame 1566 Coordinates out of bounds (-1) Warning: Frame 1568 Coordinates out of bounds (-1) Warning: Frame 1579 Coordinates out of bounds (-1) Warning: Frame 1603 Coordinates out of bounds (-1) Warning: Frame 1604 Coordinates out of bounds (-1) Warning: Frame 1605 Coordinates out of bounds (-1) Warning: Frame 1608 Coordinates out of bounds (-1) Warning: Frame 1609 Coordinates out of bounds (-1) Warning: Frame 1611 Coordinates out of bounds (-1) Warning: Frame 1691 Coordinates out of bounds (-1) Warning: Frame 1696 Coordinates out of bounds (-1) Warning: Frame 1697 Coordinates out of bounds (-1) Warning: Frame 1700 Coordinates out of bounds (-1) Warning: Frame 1709 Coordinates out of bounds (-1) Warning: Frame 1710 Coordinates out of bounds (-1) Warning: Frame 1712 Coordinates out of bounds (-1) Warning: Frame 1713 Coordinates out of bounds (-1) Warning: Frame 1714 Coordinates out of bounds (-1) Warning: Frame 1716 Coordinates out of bounds (-1) Warning: Frame 1717 Coordinates out of bounds (-1) Warning: Frame 1718 Coordinates out of bounds (-1) Warning: Frame 1721 Coordinates out of bounds (-1) Warning: Frame 1723 Coordinates out of bounds (-1) Warning: Frame 1724 Coordinates out of bounds (-1) Warning: Frame 1741 Coordinates out of bounds (-1) Warning: Frame 1876 Coordinates out of bounds (-1) Warning: Frame 1899 Coordinates out of bounds (-1) Warning: Frame 1955 Coordinates out of bounds (-1) Warning: Frame 2118 Coordinates out of bounds (-1) Warning: Frame 2123 Coordinates out of bounds (-1) Warning: Frame 2145 Coordinates out of bounds (-1) Warning: Frame 2159 Coordinates out of bounds (-1) Warning: Frame 2161 Coordinates out of bounds (-1) Warning: Frame 2162 Coordinates out of bounds (-1) Warning: Frame 2398 Coordinates out of bounds (-1) Warning: Frame 2503 Coordinates out of bounds (-1) Warning: Frame 2509 Coordinates out of bounds (-1) Warning: Frame 2522 Coordinates out of bounds (-1) Warning: Frame 2524 Coordinates out of bounds (-1) Warning: Frame 2555 Coordinates out of bounds (-1) Warning: Frame 2557 Coordinates out of bounds (-1) Warning: Frame 2573 Coordinates out of bounds (-1) Warning: Frame 2627 Coordinates out of bounds (-1) Warning: Frame 2628 Coordinates out of bounds (-1) Warning: Frame 2709 Coordinates out of bounds (-1) Warning: Frame 3127 Coordinates out of bounds (-1) Warning: Frame 3130 Coordinates out of bounds (-1) Warning: Frame 3142 Coordinates out of bounds (-1) Warning: Frame 3160 Coordinates out of bounds (-1) Warning: Frame 3190 Coordinates out of bounds (-1) Warning: Frame 3192 Coordinates out of bounds (-1) Warning: Frame 3218 Coordinates out of bounds (-1) Warning: Frame 3220 Coordinates out of bounds (-1) Warning: Frame 3222 Coordinates out of bounds (-1) Warning: Frame 3224 Coordinates out of bounds (-1) Warning: Frame 3225 Coordinates out of bounds (-1) Warning: Frame 3303 Coordinates out of bounds (-1) Warning: Frame 3305 Coordinates out of bounds (-1) Warning: Frame 3313 Coordinates out of bounds (-1) Warning: Frame 3319 Coordinates out of bounds (-1) Warning: Frame 3322 Coordinates out of bounds (-1) Warning: Frame 3324 Coordinates out of bounds (-1) Warning: Frame 3325 Coordinates out of bounds (-1) Warning: Frame 3329 Coordinates out of bounds (-1) Warning: Frame 3380 Coordinates out of bounds (-1) Warning: Frame 3430 Coordinates out of bounds (-1) Warning: Frame 3492 Coordinates out of bounds (-1) Warning: Frame 3493 Coordinates out of bounds (-1) Warning: Frame 3494 Coordinates out of bounds (-1) Warning: Frame 3506 Coordinates out of bounds (-1) Warning: Frame 3511 Coordinates out of bounds (-1) Warning: Frame 3512 Coordinates out of bounds (-1) Warning: Frame 3513 Coordinates out of bounds (-1) Warning: Frame 3684 Coordinates out of bounds (-1) Warning: Frame 3693 Coordinates out of bounds (-1) Warning: Frame 3694 Coordinates out of bounds (-1) Warning: Frame 3858 Coordinates out of bounds (-1) Warning: Frame 3860 Coordinates out of bounds (-1) Warning: Frame 3933 Coordinates out of bounds (-1) Warning: Frame 3934 Coordinates out of bounds (-1) Warning: Frame 3973 Coordinates out of bounds (-1) Warning: Frame 4133 Coordinates out of bounds (-1) Warning: Frame 4258 Coordinates out of bounds (-1) Warning: Frame 4259 Coordinates out of bounds (-1) Warning: Frame 4288 Coordinates out of bounds (-1) Warning: Frame 4305 Coordinates out of bounds (-1) Warning: Frame 4376 Coordinates out of bounds (-1) Warning: Frame 4410 Coordinates out of bounds (-1) Warning: Frame 4414 Coordinates out of bounds (-1) Warning: Frame 4444 Coordinates out of bounds (-1) Warning: Frame 4445 Coordinates out of bounds (-1) Warning: Frame 4493 Coordinates out of bounds (-1) Warning: Frame 4494 Coordinates out of bounds (-1) Warning: Frame 4550 Coordinates out of bounds (-1) Warning: Frame 4551 Coordinates out of bounds (-1) Warning: Frame 4552 Coordinates out of bounds (-1) Warning: Frame 4554 Coordinates out of bounds (-1) Warning: Frame 4691 Coordinates out of bounds (-1) Warning: Frame 4695 Coordinates out of bounds (-1) Warning: Frame 4721 Coordinates out of bounds (-1) Warning: Frame 4742 Coordinates out of bounds (-1) Warning: Frame 4748 Coordinates out of bounds (-1) Warning: Frame 4771 Coordinates out of bounds (-1) Warning: Frame 4857 Coordinates out of bounds (-1) Warning: Frame 4863 Coordinates out of bounds (-1) Warning: Frame 4872 Coordinates out of bounds (-1) Warning: Frame 4880 Coordinates out of bounds (-1) Warning: Frame 4914 Coordinates out of bounds (-1) Warning: Frame 5043 Coordinates out of bounds (-1) Warning: Frame 5046 Coordinates out of bounds (-1) Warning: Frame 5228 Coordinates out of bounds (-1) Warning: Frame 5271 Coordinates out of bounds (-1) Warning: Frame 5272 Coordinates out of bounds (-1) Warning: Frame 5273 Coordinates out of bounds (-1) Warning: Frame 5274 Coordinates out of bounds (-1) Warning: Frame 5275 Coordinates out of bounds (-1) Warning: Frame 5397 Coordinates out of bounds (-1) Warning: Frame 5398 Coordinates out of bounds (-1) Warning: Frame 5568 Coordinates out of bounds (-1) Warning: Frame 5706 Coordinates out of bounds (-1) Warning: Frame 5707 Coordinates out of bounds (-1) Warning: Frame 5713 Coordinates out of bounds (-1) Warning: Frame 5714 Coordinates out of bounds (-1) Warning: Frame 5720 Coordinates out of bounds (-1) Warning: Frame 5727 Coordinates out of bounds (-1) Warning: Frame 5768 Coordinates out of bounds (-1) Warning: Frame 5769 Coordinates out of bounds (-1) Warning: Frame 5781 Coordinates out of bounds (-1) Warning: Frame 5782 Coordinates out of bounds (-1) Warning: Frame 5783 Coordinates out of bounds (-1) Warning: Frame 5815 Coordinates out of bounds (-1) Warning: Frame 5840 Coordinates out of bounds (-1) Warning: Frame 5857 Coordinates out of bounds (-1) Warning: Frame 5859 Coordinates out of bounds (-1) Warning: Frame 5862 Coordinates out of bounds (-1) Warning: Frame 5863 Coordinates out of bounds (-1) Warning: Frame 5871 Coordinates out of bounds (-1) Warning: Frame 5876 Coordinates out of bounds (-1) Warning: Frame 5877 Coordinates out of bounds (-1) Warning: Frame 5878 Coordinates out of bounds (-1) Warning: Frame 5938 Coordinates out of bounds (-1) Warning: Frame 5939 Coordinates out of bounds (-1) Warning: Frame 6028 Coordinates out of bounds (-1) Warning: Frame 6119 Coordinates out of bounds (-1) Warning: Frame 6120 Coordinates out of bounds (-1) Warning: Frame 6121 Coordinates out of bounds (-1) Warning: Frame 6130 Coordinates out of bounds (-1) Warning: Frame 6131 Coordinates out of bounds (-1) Warning: Frame 6132 Coordinates out of bounds (-1) Warning: Frame 6133 Coordinates out of bounds (-1) Warning: Frame 6134 Coordinates out of bounds (-1) Warning: Frame 6135 Coordinates out of bounds (-1) Warning: Frame 6137 Coordinates out of bounds (-1) Warning: Frame 6138 Coordinates out of bounds (-1) Warning: Frame 6175 Coordinates out of bounds (-1) Warning: Frame 6178 Coordinates out of bounds (-1) Warning: Frame 6203 Coordinates out of bounds (-1) Warning: Frame 6208 Coordinates out of bounds (-1) Warning: Frame 6211 Coordinates out of bounds (-1) Warning: Frame 6215 Coordinates out of bounds (-1) Warning: Frame 6251 Coordinates out of bounds (-1) Warning: Frame 6253 Coordinates out of bounds (-1) Warning: Frame 6257 Coordinates out of bounds (-1) Warning: Frame 6261 Coordinates out of bounds (-1) Warning: Frame 6262 Coordinates out of bounds (-1) Warning: Frame 6294 Coordinates out of bounds (-1) Warning: Frame 6298 Coordinates out of bounds (-1) Warning: Frame 6318 Coordinates out of bounds (-1) Warning: Frame 6325 Coordinates out of bounds (-1) Warning: Frame 6406 Coordinates out of bounds (-1) Warning: Frame 6450 Coordinates out of bounds (-1) Warning: Frame 6501 Coordinates out of bounds (-1) Warning: Frame 6505 Coordinates out of bounds (-1) Warning: Frame 6528 Coordinates out of bounds (-1) Warning: Frame 6530 Coordinates out of bounds (-1) Warning: Frame 6541 Coordinates out of bounds (-1) Warning: Frame 6575 Coordinates out of bounds (-1) Warning: Frame 6608 Coordinates out of bounds (-1) Warning: Frame 6754 Coordinates out of bounds (-1) Warning: Frame 6811 Coordinates out of bounds (-1) Warning: Frame 6895 Coordinates out of bounds (-1) Warning: Frame 6896 Coordinates out of bounds (-1) Warning: Frame 6976 Coordinates out of bounds (-1) Warning: Frame 6977 Coordinates out of bounds (-1) Warning: Frame 6979 Coordinates out of bounds (-1) Warning: Frame 6984 Coordinates out of bounds (-1) Warning: Frame 6985 Coordinates out of bounds (-1) Warning: Frame 7060 Coordinates out of bounds (-1) Warning: Frame 7061 Coordinates out of bounds (-1) Warning: Frame 7092 Coordinates out of bounds (-1) Warning: Frame 7133 Coordinates 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bounds (-1) Warning: Frame 7623 Coordinates out of bounds (-1) Warning: Frame 7663 Coordinates out of bounds (-1) Warning: Frame 7664 Coordinates out of bounds (-1) Warning: Frame 7673 Coordinates out of bounds (-1) Warning: Frame 7698 Coordinates out of bounds (-1) Warning: Frame 7840 Coordinates out of bounds (-1) Warning: Frame 7841 Coordinates out of bounds (-1) Warning: Frame 7844 Coordinates out of bounds (-1) Warning: Frame 7845 Coordinates out of bounds (-1) Warning: Frame 7848 Coordinates out of bounds (-1) Warning: Frame 7849 Coordinates out of bounds (-1) Warning: Frame 8013 Coordinates out of bounds (-1) Warning: Frame 8015 Coordinates out of bounds (-1) Warning: Frame 8038 Coordinates out of bounds (-1) Warning: Frame 8040 Coordinates out of bounds (-1) Warning: Frame 8207 Coordinates out of bounds (-1) Warning: Frame 8208 Coordinates out of bounds (-1) Warning: Frame 8209 Coordinates out of bounds (-1) Warning: Frame 8210 Coordinates out of bounds (-1) Warning: Frame 8211 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Coordinates out of bounds (-1) Warning: Frame 10791 Coordinates out of bounds (-1) Warning: Frame 10805 Coordinates out of bounds (-1) Warning: Frame 10807 Coordinates out of bounds (-1) Warning: Frame 10808 Coordinates out of bounds (-1) Warning: Frame 10823 Coordinates out of bounds (-1) Warning: Frame 10828 Coordinates out of bounds (-1) Warning: Frame 10829 Coordinates out of bounds (-1) Warning: Frame 10832 Coordinates out of bounds (-1) Warning: Frame 10887 Coordinates out of bounds (-1) Warning: Frame 10923 Coordinates out of bounds (-1) Warning: Frame 10924 Coordinates out of bounds (-1) Warning: Frame 10943 Coordinates out of bounds (-1) Warning: Frame 10945 Coordinates out of bounds (-1) Warning: Frame 10946 Coordinates out of bounds (-1) Warning: Frame 10976 Coordinates out of bounds (-1) Warning: Frame 10978 Coordinates out of bounds (-1) Warning: Frame 10981 Coordinates out of bounds (-1) Warning: Frame 10985 Coordinates out of bounds (-1) Warning: Frame 11040 Coordinates out of bounds (-1) Warning: Frame 11041 Coordinates out of bounds (-1) Warning: Frame 11042 Coordinates out of bounds (-1) Warning: Frame 11063 Coordinates out of bounds (-1) Warning: Frame 11111 Coordinates out of bounds (-1) Warning: Frame 11112 Coordinates out of bounds (-1) Warning: Frame 11294 Coordinates out of bounds (-1) Warning: Frame 11319 Coordinates out of bounds (-1) Warning: Frame 11373 Coordinates out of bounds (-1) Warning: Frame 11665 Coordinates out of bounds (-1) Warning: Frame 11672 Coordinates out of bounds (-1) Warning: Frame 11674 Coordinates out of bounds (-1) Warning: Frame 11675 Coordinates out of bounds (-1) Warning: Frame 11681 Coordinates out of bounds (-1) Warning: Frame 11683 Coordinates out of bounds (-1) Warning: Frame 11697 Coordinates out of bounds (-1) Warning: Frame 11716 Coordinates out of bounds (-1) Warning: Frame 11717 Coordinates out of bounds (-1) Warning: Frame 11718 Coordinates out of bounds (-1) Warning: Frame 11720 Coordinates out of bounds (-1) Warning: Frame 11722 Coordinates out of bounds (-1) Warning: Frame 11724 Coordinates out of bounds (-1) Warning: Frame 11728 Coordinates out of bounds (-1) Warning: Frame 11732 Coordinates out of bounds (-1) Warning: Frame 11733 Coordinates out of bounds (-1) Warning: Frame 11739 Coordinates out of bounds (-1) Warning: Frame 11741 Coordinates out of bounds (-1) Warning: Frame 11765 Coordinates out of bounds (-1) Warning: Frame 11902 Coordinates out of bounds (-1) Warning: Frame 11903 Coordinates out of bounds (-1) Warning: Frame 11904 Coordinates out of bounds (-1) Warning: Frame 11923 Coordinates out of bounds (-1) Warning: Frame 11935 Coordinates out of bounds (-1) Warning: Frame 11983 Coordinates out of bounds (-1) Warning: Frame 12040 Coordinates out of bounds (-1) Warning: Frame 12043 Coordinates out of bounds (-1) Warning: Frame 12054 Coordinates out of bounds (-1) Warning: Frame 12098 Coordinates out of bounds (-1) Warning: Frame 12099 Coordinates out of bounds (-1) Warning: Frame 12140 Coordinates out of bounds (-1) Warning: Frame 12144 Coordinates out of bounds (-1) Warning: Frame 12145 Coordinates out of bounds (-1) Warning: Frame 12146 Coordinates out of bounds (-1) Warning: Frame 12147 Coordinates out of bounds (-1) Warning: Frame 12177 Coordinates out of bounds (-1) Warning: Frame 12217 Coordinates out of bounds (-1) Warning: Frame 12220 Coordinates out of bounds (-1) Warning: Frame 12223 Coordinates out of bounds (-1) Warning: Frame 12224 Coordinates out of bounds (-1) Warning: Frame 12227 Coordinates out of bounds (-1) Warning: Frame 12228 Coordinates out of bounds (-1) Warning: Frame 12229 Coordinates out of bounds (-1) Warning: Frame 12230 Coordinates out of bounds (-1) Warning: Frame 12231 Coordinates out of bounds (-1) Warning: Frame 12247 Coordinates out of bounds (-1) Warning: Frame 12248 Coordinates out of bounds (-1) Warning: Frame 12249 Coordinates out of bounds (-1) Warning: Frame 12256 Coordinates out of bounds (-1) Warning: Frame 12288 Coordinates out of bounds (-1) Warning: Frame 12396 Coordinates out of bounds (-1) Warning: Frame 12399 Coordinates out of bounds (-1) Warning: Frame 12455 Coordinates out of bounds (-1) Warning: Frame 12457 Coordinates out of bounds (-1) Warning: Frame 12458 Coordinates out of bounds (-1) Warning: Frame 12460 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 12046 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: 12560 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 12560 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: 12560 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 12560 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: 12560 data points in each dimension. Hist: Allocating histogram, total bins = 5000 Warning: Frame 205 Coordinates out of bounds (-1) Warning: Frame 206 Coordinates out of bounds (-1) Warning: Frame 2573 Coordinates out of bounds (-1) Warning: Frame 3190 Coordinates out of bounds (-1) Warning: Frame 3192 Coordinates out of bounds (-1) Warning: Frame 3506 Coordinates out of bounds (-1) Warning: Frame 4695 Coordinates out of bounds (-1) Warning: Frame 4863 Coordinates out of bounds (-1) Warning: Frame 5713 Coordinates out of bounds (-1) Warning: Frame 5714 Coordinates out of bounds (-1) Warning: Frame 6130 Coordinates out of bounds (-1) Warning: Frame 6294 Coordinates out of bounds (-1) Warning: Frame 6541 Coordinates out of bounds (-1) Warning: Frame 7618 Coordinates out of bounds (-1) Warning: Frame 7619 Coordinates out of bounds (-1) Warning: Frame 7844 Coordinates out of bounds (-1) Warning: Frame 7845 Coordinates out of bounds (-1) Warning: Frame 8209 Coordinates out of bounds (-1) Warning: Frame 8211 Coordinates out of bounds (-1) Warning: Frame 8284 Coordinates out of bounds (-1) Warning: Frame 8385 Coordinates out of bounds (-1) Warning: Frame 8386 Coordinates out of bounds (-1) Warning: Frame 8563 Coordinates out of bounds (-1) Warning: Frame 8565 Coordinates out of bounds (-1) Warning: Frame 9114 Coordinates out of bounds (-1) Warning: Frame 9194 Coordinates out of bounds (-1) Warning: Frame 9195 Coordinates out of bounds (-1) Warning: Frame 9278 Coordinates out of bounds (-1) Warning: Frame 9280 Coordinates out of bounds (-1) Warning: Frame 9295 Coordinates out of bounds (-1) Warning: Frame 9672 Coordinates out of bounds (-1) Warning: Frame 9835 Coordinates out of bounds (-1) Warning: Frame 10153 Coordinates out of bounds (-1) Warning: Frame 10352 Coordinates out of bounds (-1) Warning: Frame 11042 Coordinates out of bounds (-1) Warning: Frame 11672 Coordinates out of bounds (-1) Warning: Frame 11674 Coordinates out of bounds (-1) Warning: Frame 11675 Coordinates out of bounds (-1) Warning: Frame 11681 Coordinates out of bounds (-1) Warning: Frame 11683 Coordinates out of bounds (-1) Warning: Frame 12227 Coordinates out of bounds (-1) Warning: Frame 12229 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 12518 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 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: 12560 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 12560 TIME: Analyses took 0.0048 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 12560 dist_sugar_ox "dist_sugar_ox" (double, distance), size is 12560 dist_N3-O5p "dist_N3-O5p" (double, distance), size is 12560 COM "COM" (double, distance), size is 12560 g1 "g1" (double, torsion(gamma)), size is 12560 d1 "d1" (double, torsion(delta)), size is 12560 e1 "e1" (double, torsion(epsilon)), size is 12560 z1 "z1" (double, torsion(zeta)), size is 12560 c1 "c1" (double, torsion(chin)), size is 12560 a2 "a2" (double, torsion(alpha)), size is 12560 b2 "b2" (double, torsion(beta)), size is 12560 g2 "g2" (double, torsion(gamma)), size is 12560 d2 "d2" (double, torsion(delta)), size is 12560 c2 "c2" (double, torsion(chin)), size is 12560 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: 0.1836 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.