CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/08/15 12:15:57 | Available memory: 796.156 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.c1] Reading '../ctraj.c1' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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_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,N2,H21,H22,N7,C8,H8,N9,O6 :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,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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: 0: [traj] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 189697 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 189697 of 189697) Coordinate processing will occur on 189697 frames. TIME: Run Initialization took 0.0003 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*](43) Reference 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. 3: [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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.c1 (1-189697, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 74 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@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@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@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@O6' to ':2@N7' 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@O6' 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@O6' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' 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@O6' Atom ':1@N3' to ':2@N1' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 189697 frames and processed 189697 frames. TIME: Trajectory processing: 2.0489 s TIME: Avg. throughput= 92585.0275 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 69.4978 74 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 189647 1 4.34 0.537 2 :1@C4_:2@C5 189535 0.999 4.41 0.657 3 :1@N3_:2@C4 189299 0.998 4.5 0.599 4 :1@C4_:2@C6 189213 0.997 4.63 0.646 5 :1@N9_:2@C4 189021 0.996 4.71 0.652 6 :1@C5_:2@C4 188992 0.996 4.39 0.654 7 :1@C4_:2@N3 188976 0.996 4.46 0.601 8 :1@C4_:2@N9 188920 0.996 4.73 0.621 9 :1@C4_:2@N1 188822 0.995 4.68 0.642 10 :1@N3_:2@N3 188724 0.995 4.58 0.684 11 :1@C5_:2@C5 188683 0.995 4.37 0.769 12 :1@N9_:2@C5 188224 0.992 4.59 0.807 13 :1@C5_:2@C6 188215 0.992 4.32 0.783 14 :1@C2_:2@C4 188185 0.992 4.62 0.712 15 :1@N3_:2@C5 187932 0.991 4.74 0.673 16 :1@N3_:2@N9 187565 0.989 4.72 0.633 17 :1@N9_:2@C6 187362 0.988 4.84 0.755 18 :1@N3_:2@N1 186163 0.981 5.08 0.865 19 :1@N9_:2@N9 185967 0.98 4.97 0.71 20 :1@C4_:2@N7 185603 0.978 4.79 0.846 21 :1@C4_:2@C8 185562 0.978 4.94 0.798 22 :1@C2_:2@N9 185485 0.978 4.95 0.651 23 :1@C5_:2@N9 185374 0.977 4.97 0.685 24 :1@N9_:2@N3 185247 0.977 4.95 0.697 25 :1@N7_:2@C6 185193 0.976 4.33 1.03 26 :1@N3_:2@C6 184999 0.975 5.06 0.771 27 :1@N7_:2@C5 184953 0.975 4.52 0.929 28 :1@N3_:2@C8 184207 0.971 5.06 0.726 29 :1@N1_:2@N9 183991 0.97 5.22 0.589 30 :1@C8_:2@C4 183905 0.969 4.87 0.795 31 :1@N9_:2@N1 183686 0.968 5.03 0.649 32 :1@C8_:2@C5 183108 0.965 4.58 0.963 33 :1@N3_:2@N7 183056 0.965 5.09 0.751 34 :1@C4_:2@O6 182915 0.964 5.13 0.682 35 :1@C2_:2@C5 182669 0.963 4.9 0.849 36 :1@C6_:2@C5 182466 0.962 4.63 0.782 37 :1@C8_:2@C6 182137 0.96 4.56 1.02 38 :1@N9_:2@C2 181408 0.956 5.04 0.729 39 :1@C8_:2@N1 181034 0.954 4.79 0.889 40 :1@N2_:2@C4 181025 0.954 5.15 0.871 41 :1@C6_:2@C6 180903 0.954 4.44 0.788 42 :1@C5_:2@O6 179727 0.947 4.69 0.778 43 :1@N1_:2@C5 179685 0.947 4.83 0.888 44 :1@C2_:2@C8 179501 0.946 5.41 0.723 45 :1@C5_:2@N7 179231 0.945 4.87 0.82 46 :1@N9_:2@O6 177928 0.938 5.17 0.812 47 :1@C5_:2@C8 177713 0.937 5.18 0.769 48 :1@N2_:2@N9 177322 0.935 5.32 0.838 49 :1@N9_:2@N7 177178 0.934 4.65 0.968 50 :1@N9_:2@C8 177155 0.934 4.87 0.887 51 :1@N1_:2@C6 176764 0.932 4.78 0.99 52 :1@N7_:2@O6 175540 0.925 4.45 1.09 53 :1@C2_:2@C6 175513 0.925 5.03 0.99 54 :1@C6_:2@O6 174676 0.921 4.87 0.902 55 :1@C8_:2@N9 174050 0.918 5.21 0.748 56 :1@C2_:2@N7 173693 0.916 5.36 0.854 57 :1@N7_:2@N9 172844 0.911 5.24 0.794 58 :1@C8_:2@N7 171667 0.905 4.72 1 59 :1@C6_:2@N7 171377 0.903 5.25 0.894 60 :1@N7_:2@N7 170425 0.898 4.87 0.864 61 :1@N1_:2@C8 169702 0.895 5.61 0.763 62 :1@C8_:2@C8 169698 0.895 5.12 0.846 63 :1@C8_:2@O6 169563 0.894 4.62 1.08 64 :1@N3_:2@O6 168859 0.89 5.57 0.806 65 :1@C6_:2@C8 168826 0.89 5.55 0.791 66 :1@N1_:2@N7 166135 0.876 5.4 0.976 67 :1@N7_:2@C8 164259 0.866 5.26 0.779 68 :1@N2_:2@C5 161468 0.851 5.38 0.952 69 :1@N2_:2@C8 160870 0.848 5.78 0.85 70 :1@N1_:2@O6 155571 0.82 5.11 1.11 71 :1@O6_:2@N7 149017 0.786 5.57 1 72 :1@C2_:2@O6 144783 0.763 5.33 1.07 73 :1@N2_:2@N7 138429 0.73 5.68 0.934 74 :1@N2_:2@C6 135989 0.717 5.3 1.1 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0160 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 189697 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 189697 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 189697 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 189697 COM "COM" (double, distance), size is 189697 v_base1 "v_base1" (vector, vector), size is 189697 v_base2 "v_base2" (vector, vector), size is 189697 normalangle "normalangle" (double), size is 189697 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: 2.5647 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.