CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/30/15 19:42:29 | Available memory: 52506.4 MB INPUT: Reading Input from file 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-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c0] Reading '../ctraj.c0' as Amber NetCDF [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,C6,C5,C4,N4,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,N4,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_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,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 63 atoms, 2 res, box: Orthogonal, 1 mol, 230147 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 230147 of 230147) Coordinate processing will occur on 230147 frames. TIME: Run Initialization took 0.0007 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 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,N4,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,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 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,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-230147, 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 80 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@N4' 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@N4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' 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@N4' 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@N4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C4' Atom ':1@N6' to ':2@N4' Atom ':1@N6' to ':2@N3' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@O2' 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@N4' 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@N4' 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@N4' 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@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 230147 frames and processed 230147 frames. TIME: Trajectory processing: 1.2493 s TIME: Avg. throughput= 184215.7502 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 77.7985 80 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C6 229964 0.999 3.92 0.494 2 :1@C4_:2@N1 229956 0.999 4.22 0.431 3 :1@N9_:2@C6 229914 0.999 4.16 0.432 4 :1@C5_:2@N1 229708 0.998 4.28 0.544 5 :1@N9_:2@N1 229637 0.998 4.76 0.454 6 :1@C6_:2@N1 229582 0.998 4.33 0.591 7 :1@C4_:2@C5 229535 0.997 4.09 0.612 8 :1@C5_:2@C6 229486 0.997 4.05 0.503 9 :1@C4_:2@C2 229312 0.996 4.67 0.482 10 :1@C6_:2@C2 229136 0.996 4.09 0.566 11 :1@N9_:2@C5 229099 0.995 4.29 0.544 12 :1@C5_:2@C2 228874 0.994 4.4 0.563 13 :1@C6_:2@C6 228851 0.994 4.42 0.604 14 :1@C5_:2@C5 228632 0.993 3.89 0.624 15 :1@N3_:2@N1 228562 0.993 4.2 0.623 16 :1@N3_:2@C6 228541 0.993 4.16 0.685 17 :1@C4_:2@C4 228411 0.992 4.55 0.602 18 :1@C4_:2@N3 228404 0.992 4.83 0.548 19 :1@C6_:2@O2 228393 0.992 4.51 0.697 20 :1@C8_:2@C6 228279 0.992 4.39 0.584 21 :1@C6_:2@N3 228221 0.992 3.95 0.583 22 :1@C5_:2@N3 228177 0.991 4.3 0.538 23 :1@N6_:2@C2 228169 0.991 4.36 0.681 24 :1@C5_:2@C4 228076 0.991 4.03 0.61 25 :1@N7_:2@C6 228075 0.991 4.36 0.588 26 :1@N1_:2@C2 227722 0.989 4.05 0.677 27 :1@N7_:2@N1 227687 0.989 4.84 0.782 28 :1@N6_:2@N3 227664 0.989 3.98 0.616 29 :1@N9_:2@C2 227594 0.989 5.41 0.517 30 :1@N6_:2@N1 227575 0.989 4.92 0.666 31 :1@N9_:2@C4 227562 0.989 5.02 0.558 32 :1@C8_:2@N1 227556 0.989 5.05 0.726 33 :1@C6_:2@C5 227439 0.988 4.26 0.718 34 :1@C6_:2@C4 227389 0.988 4 0.714 35 :1@N3_:2@C2 227354 0.988 4.68 0.646 36 :1@N1_:2@N1 227260 0.987 4.27 0.665 37 :1@C4_:2@O2 227226 0.987 5.36 0.539 38 :1@C5_:2@O2 227088 0.987 5.06 0.701 39 :1@C8_:2@C5 227007 0.986 4.18 0.688 40 :1@N7_:2@C5 227003 0.986 3.98 0.691 41 :1@N1_:2@O2 226691 0.985 4.28 0.711 42 :1@N1_:2@N3 226487 0.984 4.16 0.782 43 :1@C2_:2@N1 226443 0.984 4.16 0.721 44 :1@N3_:2@C5 226423 0.984 4.55 0.76 45 :1@N1_:2@C6 226384 0.984 4.6 0.709 46 :1@N6_:2@C6 226361 0.984 5.1 0.598 47 :1@N6_:2@C4 226329 0.983 4.14 0.737 48 :1@N6_:2@O2 226295 0.983 4.63 0.882 49 :1@N7_:2@C2 226196 0.983 5 0.85 50 :1@N9_:2@N3 226145 0.983 5.53 0.541 51 :1@C2_:2@C6 226061 0.982 4.42 0.763 52 :1@C2_:2@C2 226052 0.982 4.3 0.752 53 :1@N7_:2@N3 226037 0.982 4.72 0.762 54 :1@N7_:2@C4 225566 0.98 4.19 0.723 55 :1@C5_:2@N4 225423 0.979 4.47 0.767 56 :1@N6_:2@C5 225200 0.979 4.74 0.717 57 :1@N3_:2@N3 224527 0.976 5.05 0.702 58 :1@N3_:2@O2 223739 0.972 5.18 0.652 59 :1@C8_:2@C4 223654 0.972 4.74 0.702 60 :1@C4_:2@N4 223481 0.971 5.19 0.674 61 :1@C2_:2@O2 223327 0.97 4.58 0.759 62 :1@C6_:2@N4 223312 0.97 4.38 0.874 63 :1@C2_:2@N3 222577 0.967 4.63 0.815 64 :1@N1_:2@C4 222492 0.967 4.4 0.842 65 :1@N1_:2@C5 222491 0.967 4.65 0.798 66 :1@C8_:2@C2 222361 0.966 5.5 0.762 67 :1@N3_:2@C4 222121 0.965 4.95 0.732 68 :1@C8_:2@N3 221942 0.964 5.38 0.717 69 :1@N6_:2@N4 221932 0.964 4.24 0.944 70 :1@C2_:2@C5 220142 0.957 4.7 0.824 71 :1@N9_:2@N4 218880 0.951 5.57 0.595 72 :1@N7_:2@N4 218329 0.949 4.35 0.758 73 :1@C2_:2@C4 216343 0.94 4.74 0.825 74 :1@C8_:2@N4 213485 0.928 5.01 0.684 75 :1@N1_:2@N4 207207 0.9 4.81 0.842 76 :1@N9_:2@O2 202661 0.881 6.11 0.515 77 :1@N7_:2@O2 202025 0.878 5.61 0.938 78 :1@N3_:2@N4 199448 0.867 5.56 0.688 79 :1@C2_:2@N4 195767 0.851 5.28 0.824 80 :1@C8_:2@O2 160636 0.698 6 0.75 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0159 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 230147 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 230147 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 230147 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 230147 COM "COM" (double, distance), size is 230147 v_base1 "v_base1" (vector), size is 230147 v_base2 "v_base2" (vector), size is 230147 normalangle "normalangle" (double), size is 230147 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 1.6977 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.