CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:44:11 | Available memory: 1.805 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.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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 228952 of 228952) Coordinate processing will occur on 228952 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.c0 (1-228952, 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 80 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@C8' to ':2@O2' 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 228952 frames and processed 228952 frames. TIME: Avg. throughput= 109407.3751 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 77.7628 80 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N1 228827 0.999 4.22 0.44 2 :1@C4_:2@C6 228801 0.999 3.92 0.5 3 :1@N9_:2@C6 228751 0.999 4.17 0.436 4 :1@C5_:2@N1 228574 0.998 4.29 0.553 5 :1@N9_:2@N1 228485 0.998 4.76 0.458 6 :1@C4_:2@C5 228435 0.998 4.09 0.615 7 :1@C5_:2@C6 228311 0.997 4.05 0.512 8 :1@C6_:2@N1 228273 0.997 4.33 0.595 9 :1@C4_:2@C2 228174 0.997 4.67 0.488 10 :1@N9_:2@C5 228076 0.996 4.3 0.55 11 :1@C6_:2@C2 227953 0.996 4.09 0.576 12 :1@C5_:2@C2 227674 0.994 4.4 0.569 13 :1@C5_:2@C5 227585 0.994 3.9 0.636 14 :1@C6_:2@C6 227560 0.994 4.43 0.607 15 :1@C4_:2@C4 227455 0.993 4.56 0.605 16 :1@C4_:2@N3 227330 0.993 4.84 0.551 17 :1@N3_:2@C6 227307 0.993 4.16 0.688 18 :1@N3_:2@N1 227247 0.993 4.2 0.623 19 :1@C6_:2@N3 227174 0.992 3.96 0.597 20 :1@C5_:2@C4 227050 0.992 4.03 0.622 21 :1@C5_:2@N3 227025 0.992 4.3 0.546 22 :1@C8_:2@C6 226951 0.991 4.39 0.588 23 :1@C6_:2@O2 226937 0.991 4.51 0.696 24 :1@N6_:2@C2 226684 0.99 4.36 0.682 25 :1@N7_:2@C6 226585 0.99 4.36 0.588 26 :1@N9_:2@C4 226432 0.989 5.02 0.56 27 :1@C6_:2@C4 226387 0.989 4.01 0.725 28 :1@N6_:2@N3 226370 0.989 3.99 0.626 29 :1@N1_:2@C2 226328 0.989 4.05 0.673 30 :1@C6_:2@C5 226316 0.988 4.27 0.725 31 :1@N9_:2@C2 226305 0.988 5.41 0.517 32 :1@N7_:2@N1 226211 0.988 4.84 0.78 33 :1@C8_:2@N1 226157 0.988 5.06 0.724 34 :1@N6_:2@N1 226088 0.987 4.92 0.665 35 :1@N3_:2@C2 226000 0.987 4.68 0.644 36 :1@N1_:2@N1 225839 0.986 4.27 0.661 37 :1@C4_:2@O2 225751 0.986 5.36 0.538 38 :1@C5_:2@O2 225687 0.986 5.06 0.702 39 :1@C8_:2@C5 225630 0.985 4.18 0.691 40 :1@N7_:2@C5 225530 0.985 3.98 0.693 41 :1@N1_:2@N3 225262 0.984 4.16 0.785 42 :1@N1_:2@O2 225237 0.984 4.27 0.699 43 :1@N3_:2@C5 225219 0.984 4.56 0.761 44 :1@N1_:2@C6 225065 0.983 4.6 0.711 45 :1@N6_:2@C4 225005 0.983 4.15 0.746 46 :1@C2_:2@N1 225005 0.983 4.15 0.714 47 :1@N6_:2@O2 224954 0.983 4.63 0.882 48 :1@N6_:2@C6 224910 0.982 5.1 0.598 49 :1@N9_:2@N3 224881 0.982 5.53 0.541 50 :1@N7_:2@C2 224782 0.982 5 0.847 51 :1@C2_:2@C6 224762 0.982 4.42 0.765 52 :1@C2_:2@C2 224639 0.981 4.29 0.746 53 :1@N7_:2@N3 224566 0.981 4.73 0.762 54 :1@C5_:2@N4 224296 0.98 4.47 0.773 55 :1@N7_:2@C4 224054 0.979 4.19 0.724 56 :1@N6_:2@C5 223755 0.977 4.74 0.72 57 :1@N3_:2@N3 223263 0.975 5.05 0.703 58 :1@N3_:2@O2 222595 0.972 5.17 0.647 59 :1@C4_:2@N4 222455 0.972 5.19 0.674 60 :1@C2_:2@O2 222344 0.971 4.57 0.752 61 :1@C6_:2@N4 222255 0.971 4.4 0.878 62 :1@C8_:2@C4 222188 0.97 4.74 0.704 63 :1@N1_:2@C4 221367 0.967 4.41 0.844 64 :1@N1_:2@C5 221277 0.966 4.66 0.798 65 :1@C2_:2@N3 221237 0.966 4.63 0.816 66 :1@C8_:2@C2 220987 0.965 5.5 0.759 67 :1@N3_:2@C4 220936 0.965 4.95 0.733 68 :1@N6_:2@N4 220610 0.964 4.25 0.95 69 :1@C8_:2@N3 220504 0.963 5.38 0.718 70 :1@C2_:2@C5 218886 0.956 4.7 0.824 71 :1@N9_:2@N4 217688 0.951 5.57 0.596 72 :1@N7_:2@N4 216773 0.947 4.34 0.757 73 :1@C2_:2@C4 215092 0.939 4.74 0.825 74 :1@C8_:2@N4 211999 0.926 5.01 0.683 75 :1@N1_:2@N4 206139 0.9 4.82 0.836 76 :1@N9_:2@O2 201279 0.879 6.11 0.516 77 :1@N7_:2@O2 200895 0.877 5.62 0.934 78 :1@N3_:2@N4 198370 0.866 5.57 0.685 79 :1@C2_:2@N4 194639 0.85 5.29 0.819 80 :1@C8_:2@O2 159525 0.697 6 0.745 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 228952, 'v_base2' size 228952, output size 228952 TIME: Analyses took 0.0168 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 228952 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 228952 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 228952 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 228952 COM "COM" (double, distance), size is 228952 v_base1 "v_base1" (vector, vector), size is 228952 v_base2 "v_base2" (vector, vector), size is 228952 normalangle "normalangle" (double), size is 228952 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.05%) TIME: Trajectory Process : 2.0927 s ( 99.14%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0168 s ( 0.80%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.1108 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: 2.7136 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.