CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 18:26:37 | Available memory: 3.728 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.c3] Reading '../ctraj.c3' 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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8642 of 8642) Coordinate processing will occur on 8642 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.c3 (1-8642, 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 64 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@O4' 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@O4' 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@O4' 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@C5' Atom ':2@O2' to ':1@C4' Atom ':2@O2' to ':1@O4' 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 8642 frames and processed 8642 frames. TIME: Avg. throughput= 72144.1213 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 46.6429 64 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 7416 0.858 4.95 0.865 2 :2@C6_:1@C2 7235 0.837 4.91 0.92 3 :2@C6_:1@O2 7139 0.826 4.97 1.01 4 :2@N1_:1@N1 7120 0.824 5.27 0.743 5 :2@C5_:1@O2 7050 0.816 4.63 0.978 6 :2@N1_:1@C2 6905 0.799 5.13 0.867 7 :2@C5_:1@C2 6901 0.799 4.46 0.932 8 :2@C6_:1@C6 6892 0.798 5.05 0.901 9 :2@C5_:1@N1 6852 0.793 4.56 0.831 10 :2@N1_:1@C6 6791 0.786 5.21 0.893 11 :2@C6_:1@N3 6648 0.769 5.07 0.805 12 :2@C4_:1@O2 6622 0.766 4.61 0.932 13 :2@N1_:1@O2 6587 0.762 5.17 1.08 14 :2@N1_:1@C5 6568 0.76 5.18 0.954 15 :2@N1_:1@N3 6556 0.759 5.12 0.814 16 :2@C4_:1@C2 6522 0.755 4.34 0.866 17 :2@C5_:1@C6 6500 0.752 4.78 0.859 18 :2@N1_:1@C4 6500 0.752 5.24 0.794 19 :2@C5_:1@N3 6498 0.752 4.58 0.871 20 :2@C4_:1@N1 6447 0.746 4.66 0.752 21 :2@C6_:1@C5 6425 0.743 5.2 0.87 22 :2@C2_:1@C2 6424 0.743 5 0.914 23 :2@N4_:1@O2 6394 0.74 4.66 0.936 24 :2@C2_:1@N3 6355 0.735 4.73 0.961 25 :2@N4_:1@C2 6352 0.735 4.44 0.804 26 :2@C2_:1@C4 6351 0.735 4.74 0.93 27 :2@C4_:1@N3 6350 0.735 4.15 0.901 28 :2@N3_:1@C2 6320 0.731 4.64 0.897 29 :2@C6_:1@C4 6319 0.731 5.28 0.738 30 :2@C2_:1@N1 6306 0.73 5.26 0.687 31 :2@N3_:1@O2 6295 0.728 4.94 0.959 32 :2@C2_:1@C5 6292 0.728 4.89 0.989 33 :2@N3_:1@N3 6266 0.725 4.24 0.976 34 :2@N4_:1@N3 6243 0.722 4.14 0.876 35 :2@N4_:1@N1 6226 0.72 4.87 0.723 36 :2@C2_:1@C6 6224 0.72 5.15 0.849 37 :2@C2_:1@O2 6212 0.719 5.18 1.07 38 :2@N3_:1@N1 6209 0.718 5.01 0.723 39 :2@C5_:1@C4 6166 0.713 4.83 0.787 40 :2@C4_:1@C6 6160 0.713 4.73 0.797 41 :2@C5_:1@C5 6146 0.711 4.87 0.827 42 :2@N3_:1@C4 6129 0.709 4.22 0.887 43 :2@C4_:1@C4 6121 0.708 4.27 0.817 44 :2@C2_:1@O4 6091 0.705 4.88 0.892 45 :2@O2_:1@C4 6091 0.705 5 0.931 46 :2@N3_:1@C6 6034 0.698 4.94 0.785 47 :2@N3_:1@C5 6032 0.698 4.55 0.875 48 :2@N4_:1@C4 6030 0.698 4.27 0.853 49 :2@C4_:1@C5 6029 0.698 4.53 0.827 50 :2@O2_:1@N3 5998 0.694 5.09 0.946 51 :2@N3_:1@O4 5991 0.693 4.33 0.864 52 :2@O2_:1@C5 5955 0.689 5.17 1.01 53 :2@N4_:1@C6 5949 0.688 4.93 0.869 54 :2@N1_:1@O4 5944 0.688 5.56 0.724 55 :2@O2_:1@O4 5935 0.687 4.96 0.958 56 :2@C4_:1@O4 5909 0.684 4.56 0.763 57 :2@N4_:1@O4 5870 0.679 4.46 0.87 58 :2@N4_:1@C5 5867 0.679 4.64 0.924 59 :2@C5_:1@O4 5773 0.668 5.33 0.707 60 :2@O2_:1@C2 5758 0.666 5.47 0.86 61 :2@C6_:1@O4 5659 0.655 5.77 0.647 62 :2@O2_:1@N1 5636 0.652 5.81 0.652 63 :2@O2_:1@C6 5574 0.645 5.55 0.817 64 :2@O2_:1@O2 4929 0.57 5.46 1.04 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 8642, 'v_base2' size 8642, output size 8642 TIME: Analyses took 0.0011 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 8642 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8642 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8642 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8642 COM "COM" (double, distance), size is 8642 v_base1 "v_base1" (vector, vector), size is 8642 v_base2 "v_base2" (vector, vector), size is 8642 normalangle "normalangle" (double), size is 8642 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1198 s ( 98.81%) TIME: Action Post : 0.0002 s ( 0.17%) TIME: Analysis : 0.0011 s ( 0.95%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1212 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: 0.3071 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.