CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:31:51 | Available memory: 1.218 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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 233665 of 233665) Coordinate processing will occur on 233665 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.c0 (1-233665, 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 48 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@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@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' 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@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@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 233665 frames and processed 233665 frames. TIME: Avg. throughput= 122610.7781 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 43.6783 48 # Contact Nframes Frac. Avg Stdev 1 :1@O2_:2@C5 228944 0.98 4.2 0.761 2 :1@N1_:2@C5 228884 0.98 4.45 0.616 3 :1@C2_:2@C5 228579 0.978 4.19 0.673 4 :1@N1_:2@C6 228213 0.977 4.85 0.575 5 :1@O2_:2@C6 227797 0.975 4.63 0.754 6 :1@C2_:2@C6 227330 0.973 4.77 0.665 7 :1@O2_:2@C4 227309 0.973 4.05 0.722 8 :1@C2_:2@C4 226839 0.971 4.14 0.67 9 :1@O2_:2@O4 226400 0.969 4.21 0.765 10 :1@N1_:2@C4 226257 0.968 4.7 0.68 11 :1@C2_:2@O4 226063 0.967 4.17 0.726 12 :1@N1_:2@N1 224784 0.962 5.45 0.532 13 :1@N3_:2@C5 224124 0.959 4.46 0.793 14 :1@O2_:2@N1 223677 0.957 4.89 0.761 15 :1@O2_:2@N3 223622 0.957 4.27 0.885 16 :1@N3_:2@C4 223582 0.957 4.2 0.828 17 :1@N3_:2@O4 223500 0.956 3.87 0.874 18 :1@N1_:2@O4 223435 0.956 4.86 0.753 19 :1@C2_:2@N1 222765 0.953 5.25 0.64 20 :1@C2_:2@N3 222044 0.95 4.61 0.822 21 :1@C6_:2@C5 221390 0.947 4.86 0.755 22 :1@O2_:2@C2 220626 0.944 4.7 0.889 23 :1@C6_:2@C6 218432 0.935 5.39 0.663 24 :1@C2_:2@C2 216687 0.927 5.14 0.759 25 :1@N3_:2@C6 216567 0.927 5.27 0.698 26 :1@C4_:2@O4 216029 0.925 4.25 0.967 27 :1@N1_:2@N3 215659 0.923 5.17 0.758 28 :1@C4_:2@C5 215102 0.921 4.89 0.797 29 :1@C4_:2@C4 213477 0.914 4.7 0.854 30 :1@N3_:2@N3 213205 0.912 4.76 0.858 31 :1@C6_:2@C4 213020 0.912 5.12 0.792 32 :1@C5_:2@C5 212599 0.91 5.04 0.805 33 :1@N1_:2@C2 209270 0.896 5.53 0.647 34 :1@C6_:2@O4 208581 0.893 5.09 0.86 35 :1@O4_:2@O4 207551 0.888 4.4 0.974 36 :1@C5_:2@O4 204600 0.876 4.79 0.921 37 :1@C5_:2@C4 203357 0.87 5.07 0.806 38 :1@N3_:2@N1 200311 0.857 5.76 0.64 39 :1@O2_:2@O2 199097 0.852 5.12 0.945 40 :1@O4_:2@C4 199080 0.852 5.04 0.812 41 :1@N3_:2@C2 196026 0.839 5.47 0.721 42 :1@C5_:2@C6 195986 0.839 5.74 0.648 43 :1@C4_:2@N3 191645 0.82 5.33 0.743 44 :1@C6_:2@N1 190837 0.817 6.02 0.54 45 :1@C6_:2@N3 187754 0.804 5.63 0.748 46 :1@C5_:2@N3 177682 0.76 5.71 0.725 47 :1@C6_:2@C2 167184 0.715 6.04 0.622 48 :1@N1_:2@O2 160180 0.686 5.99 0.679 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 233665, 'v_base2' size 233665, output size 233665 TIME: Analyses took 0.0164 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 233665 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 233665 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 233665 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 233665 COM "COM" (double, distance), size is 233665 v_base1 "v_base1" (vector, vector), size is 233665 v_base2 "v_base2" (vector, vector), size is 233665 normalangle "normalangle" (double), size is 233665 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0010 s ( 0.05%) TIME: Trajectory Process : 1.9057 s ( 99.09%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0164 s ( 0.85%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.9233 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: 2.5319 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.