CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 13:04:36 | Available memory: 6.491 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.c4] Reading '../ctraj.c4' 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8694 of 8694) Coordinate processing will occur on 8694 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*](37) Reference mask: [:1,2&!@H*](37) 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c4 (1-8694, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 59 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@O4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' Atom ':2@N4' to ':1@N1' Atom ':2@N4' to ':1@C6' Atom ':2@N4' to ':1@C5' Atom ':2@N4' to ':1@C4' Atom ':2@N4' to ':1@O4' Atom ':2@N4' to ':1@N3' Atom ':2@N4' to ':1@C2' Atom ':2@N4' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@O4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@O4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@N1' Atom ':2@O2' to ':1@C6' Atom ':2@O2' to ':1@C4' Atom ':2@O2' to ':1@N3' Atom ':2@O2' to ':1@C2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 8694 frames and processed 8694 frames. TIME: Avg. throughput= 72733.6613 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 45.7326 59 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 7969 0.917 4.97 0.852 2 :2@N1_:1@N1 7733 0.889 5.32 0.767 3 :2@C6_:1@C2 7600 0.874 4.95 0.938 4 :2@C6_:1@C6 7542 0.867 5.09 0.898 5 :2@C5_:1@N1 7433 0.855 4.59 0.822 6 :2@N1_:1@C6 7422 0.854 5.26 0.893 7 :2@C5_:1@C2 7386 0.85 4.53 0.956 8 :2@C5_:1@O2 7312 0.841 4.66 0.997 9 :2@C6_:1@O2 7149 0.822 4.93 1 10 :2@C5_:1@C6 7139 0.821 4.8 0.866 11 :2@N1_:1@C2 7118 0.819 5.13 0.867 12 :2@C4_:1@C2 7089 0.815 4.45 0.936 13 :2@C4_:1@N1 7067 0.813 4.7 0.754 14 :2@N1_:1@C5 6965 0.801 5.23 0.966 15 :2@C5_:1@N3 6961 0.801 4.67 0.93 16 :2@C6_:1@C5 6919 0.796 5.25 0.88 17 :2@C4_:1@O2 6909 0.795 4.65 0.955 18 :2@C6_:1@N3 6903 0.794 5.11 0.824 19 :2@N4_:1@C2 6892 0.793 4.53 0.846 20 :2@C4_:1@N3 6870 0.79 4.29 1.02 21 :2@C2_:1@N1 6855 0.788 5.3 0.717 22 :2@C2_:1@C6 6822 0.785 5.2 0.848 23 :2@N4_:1@N1 6818 0.784 4.88 0.724 24 :2@C4_:1@C6 6813 0.784 4.74 0.816 25 :2@N3_:1@N1 6807 0.783 5.05 0.741 26 :2@C2_:1@C5 6804 0.783 4.97 1.02 27 :2@N4_:1@N3 6783 0.78 4.26 0.957 28 :2@N4_:1@O2 6783 0.78 4.73 0.972 29 :2@N3_:1@C2 6748 0.776 4.71 0.948 30 :2@N1_:1@N3 6731 0.774 5.13 0.821 31 :2@C5_:1@C5 6706 0.771 4.91 0.847 32 :2@C2_:1@C2 6670 0.767 5.01 0.921 33 :2@N1_:1@C4 6666 0.767 5.26 0.808 34 :2@N3_:1@C6 6649 0.765 4.96 0.791 35 :2@C4_:1@C4 6648 0.765 4.38 0.906 36 :2@C5_:1@C4 6641 0.764 4.9 0.834 37 :2@C4_:1@C5 6625 0.762 4.58 0.859 38 :2@N3_:1@C5 6608 0.76 4.63 0.905 39 :2@C6_:1@C4 6595 0.759 5.32 0.757 40 :2@N3_:1@N3 6586 0.758 4.32 1.04 41 :2@N3_:1@C4 6586 0.758 4.34 1 42 :2@N1_:1@O2 6567 0.755 5.12 1.08 43 :2@N4_:1@C4 6565 0.755 4.34 0.896 44 :2@N4_:1@C6 6563 0.755 4.9 0.895 45 :2@C2_:1@C4 6560 0.755 4.78 0.955 46 :2@C2_:1@N3 6553 0.754 4.76 0.972 47 :2@N3_:1@O2 6461 0.743 4.92 0.961 48 :2@N4_:1@C5 6442 0.741 4.64 0.95 49 :2@N4_:1@O4 6324 0.727 4.53 0.907 50 :2@C2_:1@O2 6290 0.723 5.13 1.07 51 :2@C4_:1@O4 6283 0.723 4.65 0.836 52 :2@O2_:1@C4 6251 0.719 5.02 0.939 53 :2@N3_:1@O4 6224 0.716 4.39 0.925 54 :2@C2_:1@O4 6182 0.711 4.89 0.898 55 :2@O2_:1@N3 6143 0.707 5.09 0.938 56 :2@O2_:1@C6 6023 0.693 5.59 0.822 57 :2@O2_:1@N1 5916 0.68 5.81 0.666 58 :2@O2_:1@C2 5908 0.68 5.45 0.861 59 :2@O2_:1@O2 5022 0.578 5.41 1.05 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 8694, 'v_base2' size 8694, output size 8694 TIME: Analyses took 0.0012 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 8694 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8694 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8694 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8694 COM "COM" (double, distance), size is 8694 v_base1 "v_base1" (vector, vector), size is 8694 v_base2 "v_base2" (vector, vector), size is 8694 normalangle "normalangle" (double), size is 8694 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.1195 s ( 98.74%) TIME: Action Post : 0.0002 s ( 0.17%) TIME: Analysis : 0.0012 s ( 1.01%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1211 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: 0.1795 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.