CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 15:01:30 | Available memory: 1.540 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff14sb/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.c0] Reading '../ctraj.c0' 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,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' Mask2=':2@N1,C6,C5,C4,O4,N3,C2,O2,C7', 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,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73, center of mass. [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] [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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 76932 of 76932) Coordinate processing will occur on 76932 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,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. 9 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' 9 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2,C7' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] corresponds to 8 atoms. ----- ctraj.c0 (1-76932, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Setup 81 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@C7' 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@C7' 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@C7' 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@C7' to ':2@N1' Atom ':1@C7' to ':2@C6' Atom ':1@C7' to ':2@C5' Atom ':1@C7' to ':2@C7' Atom ':1@C7' to ':2@C4' Atom ':1@C7' to ':2@O4' Atom ':1@C7' to ':2@N3' Atom ':1@C7' to ':2@C2' Atom ':1@C7' 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@C7' 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@C7' 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@C7' 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@C7' 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@C7' 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 76932 frames and processed 76932 frames. TIME: Avg. throughput= 61294.2446 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 79.3112 81 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@N1 76926 1 4.34 0.387 2 :1@C6_:2@N1 76913 1 3.97 0.523 3 :1@N1_:2@C6 76906 1 4.04 0.424 4 :1@N1_:2@C5 76878 0.999 4.21 0.411 5 :1@N1_:2@C4 76856 0.999 4.7 0.445 6 :1@N1_:2@C2 76829 0.999 4.8 0.498 7 :1@C2_:2@C6 76826 0.999 4.38 0.461 8 :1@C2_:2@N1 76819 0.999 4.82 0.53 9 :1@C6_:2@C6 76800 0.998 4 0.519 10 :1@C6_:2@C5 76784 0.998 4.26 0.478 11 :1@C2_:2@C5 76779 0.998 4.18 0.515 12 :1@C6_:2@C2 76775 0.998 4.23 0.508 13 :1@N1_:2@N3 76775 0.998 4.91 0.531 14 :1@C6_:2@C4 76770 0.998 4.51 0.434 15 :1@C2_:2@C4 76746 0.998 4.5 0.578 16 :1@C6_:2@N3 76743 0.998 4.44 0.469 17 :1@N3_:2@C4 76720 0.997 4.1 0.585 18 :1@C5_:2@N3 76702 0.997 3.96 0.475 19 :1@C4_:2@N3 76684 0.997 3.97 0.543 20 :1@N3_:2@C5 76682 0.997 4.22 0.557 21 :1@C5_:2@C2 76681 0.997 3.99 0.544 22 :1@C4_:2@C4 76672 0.997 3.94 0.5 23 :1@C5_:2@C4 76654 0.996 4.15 0.47 24 :1@N3_:2@C6 76649 0.996 4.65 0.507 25 :1@N3_:2@N3 76611 0.996 4.43 0.667 26 :1@C4_:2@C2 76587 0.996 4.38 0.556 27 :1@C5_:2@N1 76571 0.995 4.15 0.558 28 :1@N3_:2@N1 76571 0.995 4.94 0.556 29 :1@C4_:2@O4 76531 0.995 4.14 0.574 30 :1@N1_:2@O4 76520 0.995 5.33 0.511 31 :1@C6_:2@O4 76503 0.994 5.2 0.513 32 :1@C2_:2@N3 76502 0.994 4.91 0.662 33 :1@N3_:2@O4 76501 0.994 4.27 0.701 34 :1@C5_:2@C5 76495 0.994 4.31 0.542 35 :1@C4_:2@C5 76493 0.994 4.32 0.551 36 :1@O4_:2@N3 76477 0.994 4.14 0.602 37 :1@C2_:2@C2 76449 0.994 5.1 0.673 38 :1@N3_:2@C2 76433 0.994 4.86 0.687 39 :1@C5_:2@O4 76422 0.993 4.65 0.555 40 :1@C5_:2@C6 76406 0.993 4.32 0.555 41 :1@N1_:2@C7 76403 0.993 4.58 0.525 42 :1@O4_:2@C4 76391 0.993 4.18 0.576 43 :1@C4_:2@N1 76361 0.993 4.7 0.499 44 :1@O2_:2@C6 76358 0.993 4.9 0.502 45 :1@C4_:2@C6 76315 0.992 4.68 0.532 46 :1@C2_:2@O4 76308 0.992 4.87 0.679 47 :1@O2_:2@C5 76281 0.992 4.62 0.625 48 :1@C6_:2@O2 76270 0.991 4.75 0.613 49 :1@O4_:2@O4 76257 0.991 4.11 0.649 50 :1@C7_:2@N3 76253 0.991 4.16 0.588 51 :1@C5_:2@O2 76191 0.99 4.39 0.661 52 :1@C2_:2@C7 76131 0.99 4.33 0.705 53 :1@C6_:2@C7 76107 0.989 4.94 0.607 54 :1@O4_:2@C2 76066 0.989 4.75 0.606 55 :1@C4_:2@O2 76053 0.989 4.89 0.681 56 :1@C7_:2@C4 76038 0.988 4.66 0.607 57 :1@N1_:2@O2 75951 0.987 5.49 0.607 58 :1@O2_:2@N1 75934 0.987 5.51 0.676 59 :1@O2_:2@C4 75887 0.986 5.08 0.706 60 :1@N3_:2@C7 75763 0.985 4.52 0.737 61 :1@C7_:2@C2 75746 0.985 4.03 0.722 62 :1@O4_:2@C5 75671 0.984 4.87 0.6 63 :1@C4_:2@C7 75277 0.978 4.94 0.664 64 :1@C7_:2@C5 75233 0.978 5.02 0.638 65 :1@C5_:2@C7 75178 0.977 5.1 0.66 66 :1@C7_:2@C6 75164 0.977 4.94 0.608 67 :1@C7_:2@N1 75143 0.977 4.43 0.688 68 :1@C7_:2@O4 75142 0.977 5.13 0.745 69 :1@O4_:2@N1 75131 0.977 5.33 0.514 70 :1@O4_:2@C6 74845 0.973 5.38 0.541 71 :1@O4_:2@O2 74829 0.973 5.12 0.724 72 :1@O2_:2@C7 74276 0.965 4.37 0.816 73 :1@C7_:2@O2 74266 0.965 4.02 0.849 74 :1@N3_:2@O2 73017 0.949 5.48 0.821 75 :1@O2_:2@O4 72611 0.944 5.27 0.779 76 :1@O2_:2@N3 72407 0.941 5.59 0.716 77 :1@O4_:2@C7 72149 0.938 5.45 0.677 78 :1@C2_:2@O2 70338 0.914 5.75 0.781 79 :1@O2_:2@C2 69863 0.908 5.78 0.774 80 :1@C7_:2@C7 66209 0.861 5.83 0.782 81 :1@O2_:2@O2 39112 0.508 5.96 0.97 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 76932, 'v_base2' size 76932, output size 76932 TIME: Analyses took 0.0108 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 76932 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 76932 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 76932 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 76932 COM "COM" (double, distance), size is 76932 v_base1 "v_base1" (vector, vector), size is 76932 v_base2 "v_base2" (vector, vector), size is 76932 normalangle "normalangle" (double), size is 76932 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 1.2551 s ( 99.11%) TIME: Action Post : 0.0003 s ( 0.02%) TIME: Analysis : 0.0108 s ( 0.86%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.2664 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: 1.4684 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.