CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:44:35 | Available memory: 1.376 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.c1] Reading '../ctraj.c1' 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 :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_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 :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 (1 total): 0: [traj] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 144692 of 144692) Coordinate processing will occur on 144692 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*](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] 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] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-144692, 1) ----- 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 79 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@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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 144692 frames and processed 144692 frames. TIME: Avg. throughput= 105130.9960 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 60.019 79 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N1 132633 0.917 4.73 0.942 2 :1@C2_:2@N1 130992 0.905 4.61 0.999 3 :1@N3_:2@C6 129706 0.896 4.51 1.05 4 :1@C2_:2@C6 125069 0.864 4.63 1 5 :1@N1_:2@N1 123816 0.856 4.82 0.88 6 :1@C4_:2@N1 123484 0.853 4.95 0.737 7 :1@C4_:2@C6 123252 0.852 4.6 0.898 8 :1@C2_:2@C2 120878 0.835 4.48 0.958 9 :1@N9_:2@C6 120376 0.832 4.93 0.776 10 :1@C2_:2@O2 118401 0.818 4.82 0.903 11 :1@N3_:2@C2 117666 0.813 4.79 0.796 12 :1@N9_:2@N1 117073 0.809 5.47 0.598 13 :1@C6_:2@N1 116851 0.808 5.05 0.709 14 :1@C5_:2@N1 116714 0.807 5.13 0.678 15 :1@C5_:2@C6 116662 0.806 4.9 0.779 16 :1@N1_:2@C2 116503 0.805 4.38 0.886 17 :1@N1_:2@O2 116468 0.805 4.65 0.89 18 :1@N3_:2@C5 115888 0.801 4.35 0.883 19 :1@N1_:2@C6 115503 0.798 4.9 0.824 20 :1@C2_:2@C5 114121 0.789 4.53 0.912 21 :1@C4_:2@C5 113947 0.788 4.23 0.858 22 :1@C4_:2@C2 113598 0.785 4.98 0.726 23 :1@N9_:2@C5 113574 0.785 4.53 0.865 24 :1@C6_:2@C2 113176 0.782 4.61 0.786 25 :1@C6_:2@C6 112764 0.779 5.03 0.74 26 :1@N3_:2@O2 112560 0.778 5.3 0.762 27 :1@C8_:2@C6 112292 0.776 5.37 0.708 28 :1@C5_:2@C2 111997 0.774 4.94 0.783 29 :1@C6_:2@O2 111905 0.773 4.98 0.813 30 :1@C2_:2@N3 111675 0.772 4.4 0.813 31 :1@C5_:2@C5 111418 0.77 4.39 0.874 32 :1@N3_:2@C4 111127 0.768 4.54 0.7 33 :1@N3_:2@N3 110962 0.767 4.75 0.705 34 :1@C2_:2@C4 110588 0.764 4.44 0.811 35 :1@N1_:2@N3 110417 0.763 4.13 0.791 36 :1@C4_:2@C4 110151 0.761 4.37 0.712 37 :1@N1_:2@C5 109906 0.76 4.68 0.836 38 :1@N7_:2@C6 109715 0.758 5.39 0.704 39 :1@C6_:2@C5 109438 0.756 4.62 0.827 40 :1@C4_:2@N3 109420 0.756 4.74 0.718 41 :1@N1_:2@C4 109284 0.755 4.3 0.808 42 :1@C6_:2@N3 109246 0.755 4.17 0.775 43 :1@C8_:2@C5 109106 0.754 4.79 0.891 44 :1@C5_:2@C4 109021 0.753 4.2 0.827 45 :1@C6_:2@C4 108888 0.753 4.17 0.811 46 :1@C5_:2@N3 108493 0.75 4.49 0.809 47 :1@N6_:2@C2 108485 0.75 4.95 0.736 48 :1@N9_:2@C4 108171 0.748 4.86 0.772 49 :1@N6_:2@O2 107932 0.746 5.17 0.824 50 :1@C4_:2@N4 107497 0.743 4.68 0.728 51 :1@N3_:2@N4 107466 0.743 5.05 0.686 52 :1@N7_:2@C5 107423 0.742 4.75 0.875 53 :1@C4_:2@O2 107363 0.742 5.58 0.781 54 :1@N6_:2@N1 107255 0.741 5.58 0.632 55 :1@N6_:2@N3 106874 0.739 4.4 0.791 56 :1@C6_:2@N4 106653 0.737 4.28 0.882 57 :1@C5_:2@O2 106588 0.737 5.45 0.839 58 :1@N9_:2@C2 106263 0.734 5.66 0.698 59 :1@N7_:2@N1 106005 0.733 5.72 0.701 60 :1@C5_:2@N4 105885 0.732 4.24 0.871 61 :1@N6_:2@C4 105849 0.732 4.53 0.845 62 :1@N1_:2@N4 105577 0.73 4.61 0.831 63 :1@C2_:2@N4 105414 0.729 4.91 0.806 64 :1@C8_:2@N1 104956 0.725 5.85 0.66 65 :1@N9_:2@N3 103917 0.718 5.39 0.744 66 :1@N7_:2@C4 103664 0.716 4.53 0.865 67 :1@N6_:2@N4 102994 0.712 4.38 0.941 68 :1@N6_:2@C5 102815 0.711 5.19 0.781 69 :1@C8_:2@C4 102639 0.709 4.85 0.85 70 :1@N9_:2@N4 102216 0.706 4.98 0.77 71 :1@N7_:2@N3 102175 0.706 4.99 0.889 72 :1@N7_:2@C2 102100 0.706 5.54 0.843 73 :1@N6_:2@C6 101772 0.703 5.66 0.643 74 :1@N7_:2@N4 99588 0.688 4.24 0.902 75 :1@C8_:2@N4 97717 0.675 4.66 0.887 76 :1@C8_:2@N3 97203 0.672 5.41 0.852 77 :1@C8_:2@C2 93896 0.649 5.84 0.803 78 :1@N7_:2@O2 78368 0.542 5.86 0.946 79 :1@N9_:2@O2 74820 0.517 6.09 0.849 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 144692, 'v_base2' size 144692, output size 144692 TIME: Analyses took 0.0102 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 144692 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 144692 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 144692 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 144692 COM "COM" (double, distance), size is 144692 v_base1 "v_base1" (vector, vector), size is 144692 v_base2 "v_base2" (vector, vector), size is 144692 normalangle "normalangle" (double), size is 144692 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.08%) TIME: Trajectory Process : 1.3763 s ( 99.17%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0102 s ( 0.73%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.3878 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: 1.7672 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.