CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/09/15 15:36:59 | Available memory: 79730.2 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] 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*), with fitting. [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N6,H61,H62,N7,C8,H8,N9] 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,N6,H61,H62,N7,C8,H8,N9, 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,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 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. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 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*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9] :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,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector 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,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- traj.1.01 (1-50000, 1) ----- 0% 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 98 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@N6' 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@N6' 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@N6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N3' 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@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' 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@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@C4' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' 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@C6' Atom ':1@N3' to ':2@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N3' 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@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 26.1296 s TIME: Avg. throughput= 1913.5380 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 44.6652 98 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 29764 0.595 5.2 0.978 2 :1@N9_:2@N7 29067 0.581 5.02 0.977 3 :1@N9_:2@N9 27626 0.553 5.45 0.8 4 :1@N3_:2@N7 27564 0.551 5.02 1.03 5 :1@N3_:2@C8 27487 0.55 5.04 1.1 6 :1@C4_:2@N7 27423 0.548 4.91 1.04 7 :1@N9_:2@C5 27302 0.546 5.17 0.864 8 :1@C4_:2@C8 27175 0.543 5.05 1.08 9 :1@C4_:2@C5 26716 0.534 4.93 0.922 10 :1@N3_:2@C5 26564 0.531 4.97 0.946 11 :1@N9_:2@C4 26446 0.529 5.42 0.781 12 :1@N3_:2@N9 26180 0.524 5.01 1.02 13 :1@N3_:2@C4 25897 0.518 4.98 0.939 14 :1@C4_:2@N9 25841 0.517 5.15 0.951 15 :1@C4_:2@C4 25744 0.515 5.06 0.885 16 :1@C8_:2@N7 25731 0.515 5.01 1.09 17 :1@C8_:2@C8 25342 0.507 5.3 1 18 :1@C4_:2@C6 25158 0.503 5.09 0.887 19 :1@N3_:2@C6 24778 0.496 5.18 0.941 20 :1@C5_:2@C5 24691 0.494 4.84 1.05 21 :1@C8_:2@C5 24635 0.493 5.13 0.977 22 :1@N9_:2@C6 24511 0.49 5.37 0.922 23 :1@C5_:2@N7 24261 0.485 4.9 1.13 24 :1@C2_:2@C5 24160 0.483 4.87 1.03 25 :1@C5_:2@C6 24097 0.482 4.84 0.988 26 :1@N3_:2@N3 24054 0.481 5.2 0.928 27 :1@C2_:2@N7 23941 0.479 5.07 1.07 28 :1@C4_:2@N6 23909 0.478 5.27 0.926 29 :1@C2_:2@C4 23845 0.477 4.81 1.05 30 :1@C4_:2@N3 23531 0.471 5.32 0.852 31 :1@C8_:2@C4 23495 0.47 5.47 0.869 32 :1@C8_:2@N9 23444 0.469 5.58 0.831 33 :1@C5_:2@C4 23408 0.468 5 0.971 34 :1@C2_:2@C8 23327 0.467 5.12 1.09 35 :1@C2_:2@N9 23287 0.466 4.95 1.07 36 :1@C4_:2@N1 23276 0.466 5.36 0.93 37 :1@C2_:2@C6 23243 0.465 4.95 1.02 38 :1@N7_:2@N7 23157 0.463 4.98 1.15 39 :1@C5_:2@N6 23132 0.463 4.9 1 40 :1@N7_:2@C5 23108 0.462 4.96 1.04 41 :1@C6_:2@C6 22996 0.46 4.71 1.06 42 :1@C5_:2@N1 22964 0.459 5.04 0.982 43 :1@N3_:2@N6 22964 0.459 5.41 0.991 44 :1@C5_:2@C8 22954 0.459 5.14 1.07 45 :1@C8_:2@C6 22780 0.456 5.18 1.04 46 :1@C2_:2@N3 22747 0.455 4.85 1.05 47 :1@C6_:2@C5 22656 0.453 4.8 1.1 48 :1@N3_:2@C2 22605 0.452 5.34 0.958 49 :1@N3_:2@N1 22565 0.451 5.35 0.968 50 :1@C4_:2@C2 22525 0.451 5.41 0.916 51 :1@N7_:2@C6 22509 0.45 4.89 1.05 52 :1@N1_:2@C6 22428 0.449 4.77 1.05 53 :1@N9_:2@N6 22399 0.448 5.44 0.951 54 :1@N1_:2@C5 22377 0.448 4.82 1.07 55 :1@C2_:2@C2 22370 0.447 4.97 1.04 56 :1@C2_:2@N1 22334 0.447 5.02 1.03 57 :1@C6_:2@N1 22321 0.446 4.75 1.02 58 :1@C6_:2@N6 22319 0.446 4.82 1.06 59 :1@N9_:2@N3 22306 0.446 5.73 0.822 60 :1@C5_:2@N9 22149 0.443 5.2 0.956 61 :1@N1_:2@N1 22140 0.443 4.76 1.04 62 :1@C5_:2@C2 22042 0.441 5.16 0.991 63 :1@N7_:2@C4 22019 0.44 5.29 0.939 64 :1@N1_:2@C4 21949 0.439 4.78 1.07 65 :1@N7_:2@N6 21827 0.437 4.81 1.11 66 :1@C5_:2@N3 21767 0.435 5.15 0.935 67 :1@C8_:2@N6 21618 0.432 5.12 1.09 68 :1@N1_:2@C2 21609 0.432 4.69 1.05 69 :1@C2_:2@N6 21592 0.432 5.17 1.08 70 :1@C6_:2@C4 21570 0.431 4.85 1.03 71 :1@C6_:2@N7 21560 0.431 5.05 1.11 72 :1@N1_:2@N6 21512 0.43 4.97 1.08 73 :1@C6_:2@C2 21509 0.43 4.78 1.03 74 :1@N1_:2@N3 21428 0.429 4.7 1.06 75 :1@N1_:2@N7 21394 0.428 5.15 1.08 76 :1@N7_:2@C8 21272 0.425 5.27 0.999 77 :1@N7_:2@N1 21152 0.423 5.17 1.09 78 :1@C6_:2@N3 20867 0.417 4.83 0.996 79 :1@N6_:2@C6 20740 0.415 4.71 1.13 80 :1@N1_:2@N9 20695 0.414 5.08 1.02 81 :1@N6_:2@N1 20650 0.413 4.63 1.1 82 :1@N7_:2@N9 20620 0.412 5.49 0.888 83 :1@N6_:2@N6 20617 0.412 4.74 1.17 84 :1@N7_:2@N3 20031 0.401 5.5 1 85 :1@C6_:2@N9 20006 0.4 5.17 0.972 86 :1@N6_:2@C2 19839 0.397 4.71 1.1 87 :1@N1_:2@C8 19808 0.396 5.25 1.03 88 :1@N7_:2@C2 19725 0.395 5.38 1.08 89 :1@C6_:2@C8 19712 0.394 5.26 1.03 90 :1@N9_:2@N1 19709 0.394 5.56 0.942 91 :1@N6_:2@C5 19671 0.393 4.97 1.09 92 :1@C8_:2@N3 19172 0.383 5.68 0.914 93 :1@N6_:2@C4 18786 0.376 5.06 1 94 :1@N9_:2@C2 18731 0.375 5.67 0.92 95 :1@C8_:2@N1 18709 0.374 5.37 1.05 96 :1@N6_:2@N7 17541 0.351 5.3 1.03 97 :1@C8_:2@C2 17086 0.342 5.52 0.995 98 :1@N6_:2@C8 15001 0.3 5.56 0.864 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0024 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector), size is 50000 v_base2 "v_base2" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 26.5050 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.