CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:16:21 | Available memory: 2.099 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,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2' Mask2=':2@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 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] [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, 59 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 126351 of 126351) Coordinate processing will occur on 126351 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 :1@N1,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 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 7 atoms. ----- ctraj.c1 (1-126351, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 native contacts: 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@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' 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@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' 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@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' 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@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@O4' to ':2@N1' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' Atom ':1@O4' 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@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' 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@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 126351 frames and processed 126351 frames. TIME: Avg. throughput= 111887.2264 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 60.633 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 125637 0.994 4.36 0.578 2 :1@C6_:2@C6 125439 0.993 4.23 0.649 3 :1@N1_:2@N1 125369 0.992 4.67 0.531 4 :1@C6_:2@C5 125207 0.991 4.04 0.653 5 :1@N1_:2@C5 125189 0.991 4.52 0.587 6 :1@C6_:2@N1 124677 0.987 4.7 0.636 7 :1@N1_:2@C4 124390 0.984 5 0.567 8 :1@C6_:2@C4 124305 0.984 4.38 0.604 9 :1@C5_:2@C5 123950 0.981 3.95 0.736 10 :1@C5_:2@C4 123946 0.981 3.89 0.698 11 :1@C6_:2@N3 123859 0.98 4.8 0.625 12 :1@N1_:2@C2 123841 0.98 5.09 0.54 13 :1@C2_:2@C6 123774 0.98 4.58 0.766 14 :1@C5_:2@N3 123730 0.979 4.21 0.717 15 :1@C2_:2@N1 123694 0.979 4.54 0.754 16 :1@C6_:2@C2 123661 0.979 4.97 0.644 17 :1@N1_:2@N3 123646 0.979 5.2 0.57 18 :1@C5_:2@C6 123295 0.976 4.34 0.708 19 :1@C4_:2@N3 123014 0.974 4.01 0.749 20 :1@C5_:2@C2 122956 0.973 4.58 0.776 21 :1@C4_:2@C4 122888 0.973 4.08 0.779 22 :1@C2_:2@C5 122683 0.971 4.84 0.762 23 :1@C6_:2@O4 122677 0.971 4.76 0.643 24 :1@C5_:2@O4 122462 0.969 4.1 0.712 25 :1@C5_:2@N1 122422 0.969 4.63 0.743 26 :1@C2_:2@C2 122280 0.968 4.76 0.733 27 :1@C4_:2@C5 121867 0.965 4.36 0.758 28 :1@C4_:2@C2 121838 0.964 4.25 0.753 29 :1@N3_:2@N3 121603 0.962 4.41 0.815 30 :1@N3_:2@C2 121313 0.96 4.31 0.784 31 :1@C2_:2@N3 121244 0.96 5.01 0.741 32 :1@C4_:2@O4 121161 0.959 4.35 0.827 33 :1@C2_:2@C4 120861 0.957 5.09 0.737 34 :1@O4_:2@N3 120853 0.956 3.97 0.802 35 :1@C4_:2@C6 120796 0.956 4.58 0.68 36 :1@N1_:2@O4 120781 0.956 5.57 0.596 37 :1@N3_:2@C4 120756 0.956 4.62 0.82 38 :1@N3_:2@N1 120656 0.955 4.42 0.753 39 :1@N3_:2@C6 120649 0.955 4.62 0.75 40 :1@N3_:2@C5 120529 0.954 4.7 0.797 41 :1@C4_:2@N1 120324 0.952 4.52 0.7 42 :1@O4_:2@C4 120274 0.952 4.19 0.819 43 :1@C4_:2@O2 119685 0.947 4.64 0.821 44 :1@O4_:2@C2 119222 0.944 4.35 0.81 45 :1@N3_:2@O2 119168 0.943 4.59 0.796 46 :1@O4_:2@O4 118890 0.941 4.28 0.914 47 :1@N1_:2@O2 118758 0.94 5.68 0.576 48 :1@C2_:2@O2 118508 0.938 5.13 0.72 49 :1@C5_:2@O2 118206 0.936 5.2 0.839 50 :1@O4_:2@C5 118013 0.934 4.78 0.741 51 :1@O2_:2@N1 117972 0.934 4.84 0.834 52 :1@O2_:2@C6 117851 0.933 5.04 0.827 53 :1@O4_:2@N1 117488 0.93 4.94 0.737 54 :1@O4_:2@O2 117475 0.93 4.57 0.935 55 :1@O4_:2@C6 117090 0.927 5.14 0.663 56 :1@N3_:2@O4 116445 0.922 5.09 0.824 57 :1@C6_:2@O2 116322 0.921 5.66 0.685 58 :1@O2_:2@C2 115100 0.911 5.12 0.841 59 :1@O2_:2@C5 112630 0.891 5.47 0.826 60 :1@C2_:2@O4 112193 0.888 5.65 0.7 61 :1@O2_:2@O2 110520 0.875 5.32 0.841 62 :1@O2_:2@N3 108762 0.861 5.53 0.815 63 :1@O2_:2@C4 104490 0.827 5.71 0.8 64 :1@O2_:2@O4 71752 0.568 6.08 0.753 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 126351, 'v_base2' size 126351, output size 126351 TIME: Analyses took 0.0090 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 126351 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 126351 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 126351 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 126351 COM "COM" (double, distance), size is 126351 v_base1 "v_base1" (vector, vector), size is 126351 v_base2 "v_base2" (vector, vector), size is 126351 normalangle "normalangle" (double), size is 126351 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.09%) TIME: Trajectory Process : 1.1293 s ( 99.10%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0090 s ( 0.79%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.1395 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: 1.5256 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.