CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/07/16 23:29:58 | Available memory: 1.342 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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,C6,C5,C4,O4,N3,C2,O2 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,C6,C5,C4,O4,N3,C2,O2', 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, 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,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] [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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] Reading '../../traj.1.01' as Amber NetCDF [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3298 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped topology: 62 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](39) Reference mask: [:1,2&!@H*](39) 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,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- traj.1.01 (1-50000, 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,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 71 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@O4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@O4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C4' Atom ':1@N6' to ':2@O4' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Avg. throughput= 60.3296 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 41.462 71 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 34906 0.698 4.89 0.893 2 :1@N3_:2@C6 34881 0.698 4.77 0.993 3 :1@N9_:2@C5 34172 0.683 4.72 0.874 4 :1@N3_:2@C5 34057 0.681 4.79 0.966 5 :1@C4_:2@C6 33783 0.676 4.73 0.967 6 :1@C4_:2@C5 33464 0.669 4.58 0.922 7 :1@N3_:2@N1 33232 0.665 4.85 0.97 8 :1@N9_:2@N1 32247 0.645 5.28 0.774 9 :1@N3_:2@C4 32081 0.642 4.98 0.882 10 :1@C4_:2@C4 31991 0.64 4.75 0.823 11 :1@C4_:2@N1 31903 0.638 4.95 0.914 12 :1@N9_:2@C4 31879 0.638 5.04 0.786 13 :1@C2_:2@C6 31778 0.636 4.93 0.971 14 :1@C8_:2@C5 31359 0.627 4.71 0.996 15 :1@N3_:2@C2 31262 0.625 5.01 0.905 16 :1@C2_:2@C5 31255 0.625 4.91 0.975 17 :1@N3_:2@N3 31087 0.622 5.07 0.86 18 :1@C5_:2@C5 31047 0.621 4.56 0.987 19 :1@C4_:2@O4 31000 0.62 5.05 0.834 20 :1@C8_:2@C6 30785 0.616 5.06 0.929 21 :1@C2_:2@N1 30777 0.616 4.8 1.04 22 :1@C4_:2@N3 30697 0.614 4.96 0.821 23 :1@C5_:2@C4 30527 0.611 4.48 0.962 24 :1@N9_:2@O4 30334 0.607 5.31 0.801 25 :1@C2_:2@C4 30192 0.604 4.88 0.951 26 :1@C4_:2@C2 30170 0.603 5.05 0.845 27 :1@C5_:2@O4 30110 0.602 4.59 0.939 28 :1@C5_:2@C6 29934 0.599 4.85 0.941 29 :1@C2_:2@N3 29888 0.598 4.83 0.977 30 :1@C2_:2@C2 29753 0.595 4.76 1.06 31 :1@N3_:2@O4 29746 0.595 5.31 0.925 32 :1@N9_:2@N3 29711 0.594 5.36 0.757 33 :1@C6_:2@C4 29506 0.59 4.52 0.986 34 :1@C8_:2@C4 29502 0.59 4.84 0.916 35 :1@C6_:2@O4 29444 0.589 4.61 1.01 36 :1@N9_:2@C2 29417 0.588 5.49 0.726 37 :1@C6_:2@C5 29267 0.585 4.81 0.92 38 :1@N1_:2@C4 29195 0.584 4.74 0.946 39 :1@N1_:2@C5 29141 0.583 4.99 0.908 40 :1@C5_:2@N3 29018 0.58 4.65 0.952 41 :1@N7_:2@C4 28779 0.576 4.52 0.997 42 :1@N1_:2@C6 28696 0.574 5.15 0.894 43 :1@N1_:2@N3 28565 0.571 4.59 1.02 44 :1@N7_:2@O4 28436 0.569 4.49 0.981 45 :1@N1_:2@O4 28221 0.564 4.89 0.985 46 :1@C6_:2@N3 28085 0.562 4.46 1.01 47 :1@C2_:2@O4 28058 0.561 5.12 1.01 48 :1@C5_:2@N1 28042 0.561 5 0.941 49 :1@C8_:2@N1 27861 0.557 5.46 0.844 50 :1@C6_:2@C6 27781 0.556 5.08 0.865 51 :1@N6_:2@O4 27740 0.555 4.61 1.07 52 :1@C5_:2@C2 27617 0.552 4.89 0.956 53 :1@N1_:2@N1 27610 0.552 4.92 0.996 54 :1@C8_:2@N3 27542 0.551 5.25 0.884 55 :1@N3_:2@O2 27528 0.551 5.3 0.862 56 :1@N1_:2@C2 27432 0.549 4.62 1.08 57 :1@N7_:2@N3 27371 0.547 4.87 0.987 58 :1@N6_:2@C4 27183 0.544 4.68 0.987 59 :1@C4_:2@O2 26540 0.531 5.46 0.789 60 :1@C6_:2@C2 26524 0.53 4.67 1.02 61 :1@C2_:2@O2 26521 0.53 4.82 1.01 62 :1@C8_:2@C2 26313 0.526 5.55 0.859 63 :1@N6_:2@C5 26181 0.524 5.21 0.846 64 :1@C6_:2@N1 26171 0.523 4.98 0.925 65 :1@N6_:2@N3 25872 0.517 4.52 1.03 66 :1@N7_:2@C2 25729 0.515 5.27 0.982 67 :1@N1_:2@O2 24938 0.499 4.6 1.03 68 :1@C5_:2@O2 24721 0.494 5.26 0.921 69 :1@C6_:2@O2 24232 0.485 4.83 1 70 :1@N9_:2@O2 23350 0.467 5.93 0.709 71 :1@C8_:2@O2 18962 0.379 5.86 0.85 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 50000, 'v_base2' size 50000, output size 50000 TIME: Analyses took 0.0062 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 50000 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector, vector), size is 50000 v_base2 "v_base2" (vector, vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 828.7804 s ( 99.98%) TIME: Action Post : 0.1594 s ( 0.02%) TIME: Analysis : 0.0062 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0010 s ( 0.00%) TIME: Run Total 828.9471 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 833.7203 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.