CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:44:04 | Available memory: 3.928 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.c2] Reading '../ctraj.c2' 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':1@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_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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [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] [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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 (1 total): 0: [traj] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11698 of 11698) Coordinate processing will occur on 11698 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*](40) Reference mask: [:1,2&!@H*](40) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [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. 6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c2 (1-11698, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 48 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@O6' to ':1@N1' Atom ':2@O6' to ':1@C6' Atom ':2@O6' to ':1@N3' Atom ':2@O6' to ':1@C2' Atom ':2@O6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' 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@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N2' to ':1@N1' Atom ':2@N2' to ':1@N3' Atom ':2@N2' to ':1@C2' Atom ':2@N2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 11698 frames and processed 11698 frames. TIME: Avg. throughput= 64553.5113 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 39.8036 48 # Contact Nframes Frac. Avg Stdev 1 :2@C4_:1@N1 10477 0.896 5.01 0.638 2 :2@N9_:1@N1 10386 0.888 5.42 0.643 3 :2@C5_:1@N1 10381 0.887 5.13 0.694 4 :2@N3_:1@N1 10335 0.883 4.87 0.826 5 :2@C5_:1@C2 10290 0.88 4.97 0.882 6 :2@C6_:1@C2 10217 0.873 4.81 0.775 7 :2@C4_:1@C6 10206 0.872 4.7 0.696 8 :2@C2_:1@N1 10191 0.871 4.86 0.902 9 :2@C6_:1@N1 10187 0.871 5.2 0.596 10 :2@C4_:1@C2 10182 0.87 4.97 0.773 11 :2@N1_:1@N1 10140 0.867 5.07 0.673 12 :2@C2_:1@C6 10138 0.867 4.85 0.868 13 :2@C5_:1@C6 10124 0.865 4.91 0.646 14 :2@N3_:1@C2 10108 0.864 4.81 0.802 15 :2@C6_:1@N3 10097 0.863 4.32 0.857 16 :2@N1_:1@C6 10064 0.86 5.07 0.757 17 :2@C6_:1@C6 10064 0.86 5.12 0.697 18 :2@N1_:1@C2 10037 0.858 4.57 0.753 19 :2@C2_:1@C2 10023 0.857 4.55 0.876 20 :2@C5_:1@N3 10013 0.856 4.62 0.891 21 :2@O6_:1@C2 9999 0.855 5.17 0.785 22 :2@O6_:1@N3 9980 0.853 4.61 0.783 23 :2@N1_:1@C4 9962 0.852 4.15 0.789 24 :2@N1_:1@N3 9936 0.849 4.1 0.796 25 :2@C6_:1@O2 9904 0.847 5.15 0.937 26 :2@N1_:1@O2 9877 0.844 4.91 0.853 27 :2@C2_:1@N3 9870 0.844 4.25 0.794 28 :2@N3_:1@O2 9827 0.84 5.25 0.822 29 :2@N3_:1@N3 9814 0.839 4.59 0.779 30 :2@O6_:1@N1 9811 0.839 5.69 0.702 31 :2@N2_:1@N3 9793 0.837 4.59 0.823 32 :2@C4_:1@N3 9790 0.837 4.7 0.811 33 :2@C4_:1@O2 9784 0.836 5.44 0.846 34 :2@C2_:1@O2 9773 0.835 4.9 0.918 35 :2@N7_:1@N1 9696 0.829 5.46 0.968 36 :2@C8_:1@N1 9638 0.824 5.59 0.888 37 :2@N2_:1@C2 9628 0.823 4.71 1.03 38 :2@O6_:1@C6 9588 0.82 5.64 0.834 39 :2@N9_:1@C2 9571 0.818 5.5 0.768 40 :2@C5_:1@O2 9484 0.811 5.3 0.99 41 :2@O6_:1@O2 9321 0.797 5.35 1.05 42 :2@N2_:1@N1 9288 0.794 4.94 1.06 43 :2@N7_:1@C2 9287 0.794 5.35 1.02 44 :2@N2_:1@O2 8926 0.763 4.78 1.08 45 :2@C8_:1@C2 8533 0.729 5.56 0.925 46 :2@N9_:1@O2 7666 0.655 5.72 0.888 47 :2@N7_:1@O2 7122 0.609 5.28 1.11 48 :2@C8_:1@O2 6094 0.521 5.43 0.944 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 11698, 'v_base2' size 11698, output size 11698 TIME: Analyses took 0.0016 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 11698 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 11698 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 11698 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 11698 COM "COM" (double, distance), size is 11698 v_base2 "v_base2" (vector, vector), size is 11698 v_base1 "v_base1" (vector, vector), size is 11698 normalangle "normalangle" (double), size is 11698 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1812 s ( 99.01%) TIME: Action Post : 0.0002 s ( 0.09%) TIME: Analysis : 0.0016 s ( 0.85%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1830 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: 0.4238 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.