CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:44:43 | Available memory: 1.569 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c5] Reading '../ctraj.c5' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9', contacts set up based on first frame. Distance cutoff is 7 Angstroms, imaging is on. Mask selection will not include solvent. Data set name: Contacts_00002 Saving minimum observed distances in set 'Contacts_00002[mindist]' Contact stats will be written to 'STDOUT' Contact res pairs will be written to 'STDOUT' [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :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,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] VECTORMATH: Calculating Angle from dot product of vectors v_base1 and v_base2 Vectors will be normalized. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 23026 of 23026) Coordinate processing will occur on 23026 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](42) Reference mask: [:1,2&!@H*](42) 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. 3: [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c5 (1-23026, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 56 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@N9' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@N9' Atom ':1@N7' to ':2@C8' Atom ':1@N7' to ':2@N7' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@N7' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@O6' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N9' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@O6' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 23026 frames and processed 23026 frames. TIME: Avg. throughput= 127068.0426 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 1.97485 56 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 2106 0.0915 6 0.967 2 :1@N9_:2@N7 1779 0.0773 5.75 1.05 3 :1@N3_:2@C8 1778 0.0772 6.3 0.493 4 :1@C8_:2@C8 1703 0.074 5.76 1.11 5 :1@C8_:2@N7 1624 0.0705 5.49 1.26 6 :1@C4_:2@C8 1393 0.0605 6.16 0.708 7 :1@C2_:2@C8 1289 0.056 6.33 0.505 8 :1@N3_:2@N9 1258 0.0546 6.52 0.326 9 :1@C8_:2@C5 1204 0.0523 5.81 0.963 10 :1@N9_:2@N3 1176 0.0511 6.57 0.304 11 :1@N9_:2@C5 1170 0.0508 6.03 0.781 12 :1@N9_:2@N9 1147 0.0498 6.18 0.712 13 :1@C2_:2@N9 1145 0.0497 6.4 0.389 14 :1@N7_:2@N7 1117 0.0485 5.65 1.07 15 :1@C8_:2@N9 1115 0.0484 6.05 0.723 16 :1@C4_:2@N7 1065 0.0463 6.01 0.773 17 :1@N7_:2@C8 1064 0.0462 5.81 0.881 18 :1@C8_:2@O6 1033 0.0449 5.78 0.892 19 :1@C8_:2@C6 1014 0.044 5.92 0.804 20 :1@N3_:2@N7 991 0.043 6.36 0.464 21 :1@C8_:2@C4 954 0.0414 6.13 0.641 22 :1@N9_:2@C4 923 0.0401 6.29 0.564 23 :1@C5_:2@C8 901 0.0391 6.1 0.671 24 :1@C8_:2@N3 874 0.038 6.54 0.408 25 :1@N9_:2@C6 851 0.037 6.15 0.602 26 :1@N9_:2@O6 827 0.0359 6.07 0.656 27 :1@N9_:2@C2 818 0.0355 6.57 0.415 28 :1@C5_:2@N7 796 0.0346 5.92 0.758 29 :1@C8_:2@N1 759 0.033 6.31 0.54 30 :1@N7_:2@O6 733 0.0318 5.98 0.742 31 :1@N7_:2@C5 716 0.0311 5.95 0.689 32 :1@N7_:2@N9 715 0.0311 6.28 0.456 33 :1@C4_:2@N9 715 0.0311 6.46 0.405 34 :1@C8_:2@C2 685 0.0297 6.43 0.502 35 :1@N1_:2@C8 664 0.0288 6.48 0.421 36 :1@N7_:2@C6 628 0.0273 6.15 0.614 37 :1@C2_:2@N7 580 0.0252 6.53 0.395 38 :1@C6_:2@C8 577 0.0251 6.49 0.39 39 :1@N7_:2@C4 535 0.0232 6.41 0.398 40 :1@N9_:2@N1 520 0.0226 6.45 0.417 41 :1@C4_:2@C5 481 0.0209 6.33 0.443 42 :1@C5_:2@N9 475 0.0206 6.53 0.322 43 :1@C6_:2@N7 453 0.0197 6.44 0.394 44 :1@C5_:2@C5 397 0.0172 6.36 0.375 45 :1@C4_:2@O6 341 0.0148 6.44 0.445 46 :1@C5_:2@O6 339 0.0147 6.36 0.506 47 :1@N1_:2@N7 287 0.0125 6.62 0.337 48 :1@C4_:2@C6 272 0.0118 6.59 0.354 49 :1@C4_:2@C4 244 0.0106 6.61 0.264 50 :1@N6_:2@N7 220 0.00955 6.59 0.329 51 :1@C5_:2@C6 211 0.00916 6.5 0.374 52 :1@N6_:2@C8 205 0.0089 6.59 0.393 53 :1@N3_:2@C5 205 0.0089 6.71 0.248 54 :1@C6_:2@N9 189 0.00821 6.61 0.333 55 :1@C5_:2@C4 152 0.0066 6.75 0.218 56 :1@N3_:2@C4 60 0.00261 6.85 0.124 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 23026, 'v_base2' size 23026, output size 23026 TIME: Analyses took 0.0015 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 23026 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 23026 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 23026 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 23026 COM "COM" (double, distance), size is 23026 v_base1 "v_base1" (vector, vector), size is 23026 v_base2 "v_base2" (vector, vector), size is 23026 normalangle "normalangle" (double), size is 23026 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1812 s ( 99.06%) TIME: Action Post : 0.0002 s ( 0.09%) TIME: Analysis : 0.0015 s ( 0.80%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1829 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.2649 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.