CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 11:49:23 | Available memory: 1.222 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.c4] Reading '../ctraj.c4' 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,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482) Coordinate processing will occur on 7482 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,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c4 (1-7482, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,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@N4' to ':2@N1' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' 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 7482 frames and processed 7482 frames. TIME: Avg. throughput= 82607.3996 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 28.8118 64 # Contact Nframes Frac. Avg Stdev 1 :1@O2_:2@C6 4398 0.588 5.04 0.985 2 :1@O2_:2@N1 4322 0.578 5.42 0.958 3 :1@N1_:2@C6 4308 0.576 5.08 0.991 4 :1@C2_:2@C6 4254 0.569 4.94 1.02 5 :1@C2_:2@N1 4134 0.553 5.22 0.87 6 :1@N1_:2@N1 4096 0.547 5.38 0.803 7 :1@O2_:2@C5 3992 0.534 4.68 1.06 8 :1@N3_:2@N1 3822 0.511 5.06 0.876 9 :1@N3_:2@C6 3767 0.503 4.92 0.917 10 :1@C2_:2@C5 3731 0.499 4.51 1.05 11 :1@O2_:2@C2 3714 0.496 5.46 0.98 12 :1@C6_:2@C6 3706 0.495 5.09 0.944 13 :1@N1_:2@C5 3679 0.492 4.76 0.943 14 :1@C6_:2@N1 3664 0.49 5.23 0.888 15 :1@C4_:2@N1 3648 0.488 5.03 0.891 16 :1@O2_:2@C4 3609 0.482 4.75 0.976 17 :1@O2_:2@N3 3560 0.476 5.17 0.968 18 :1@C5_:2@N1 3559 0.476 5.06 0.975 19 :1@C2_:2@C2 3557 0.475 5.15 0.895 20 :1@N3_:2@C2 3478 0.465 4.74 0.957 21 :1@C4_:2@C6 3457 0.462 5.01 0.873 22 :1@N3_:2@C5 3445 0.46 4.45 0.977 23 :1@C5_:2@C6 3405 0.455 5.07 0.919 24 :1@C4_:2@C2 3366 0.45 4.62 0.95 25 :1@N4_:2@N1 3366 0.45 5.23 0.822 26 :1@C2_:2@C4 3356 0.449 4.46 0.872 27 :1@N3_:2@O2 3353 0.448 5.17 0.946 28 :1@O2_:2@O4 3327 0.445 4.8 0.949 29 :1@C6_:2@C5 3316 0.443 4.95 0.878 30 :1@N4_:2@O2 3311 0.443 4.8 0.99 31 :1@C4_:2@O2 3310 0.442 4.95 0.919 32 :1@C2_:2@N3 3307 0.442 4.77 0.875 33 :1@N1_:2@C2 3292 0.44 5.39 0.684 34 :1@N1_:2@C4 3283 0.439 4.94 0.777 35 :1@N4_:2@C2 3271 0.437 4.62 0.95 36 :1@C5_:2@C2 3252 0.435 4.88 0.967 37 :1@N3_:2@C4 3233 0.432 4.1 0.905 38 :1@N3_:2@N3 3233 0.432 4.23 0.913 39 :1@C2_:2@O4 3192 0.427 4.65 0.803 40 :1@C4_:2@C5 3187 0.426 4.64 0.873 41 :1@C6_:2@C2 3179 0.425 5.27 0.797 42 :1@C2_:2@O2 3153 0.421 5.61 0.87 43 :1@N1_:2@N3 3126 0.418 5.2 0.684 44 :1@C4_:2@N3 3123 0.417 4.2 0.883 45 :1@C5_:2@O2 3119 0.417 5.16 0.945 46 :1@C5_:2@C5 3102 0.415 4.89 0.843 47 :1@N3_:2@O4 3100 0.414 4.22 0.847 48 :1@N4_:2@C6 3090 0.413 5.37 0.743 49 :1@C4_:2@C4 3079 0.412 4.25 0.852 50 :1@N4_:2@N3 3073 0.411 4.16 0.919 51 :1@N1_:2@O4 3068 0.41 5.24 0.726 52 :1@C6_:2@C4 3057 0.409 5.06 0.799 53 :1@C6_:2@N3 3015 0.403 5.19 0.741 54 :1@C5_:2@N3 3007 0.402 4.7 0.842 55 :1@C5_:2@C4 2987 0.399 4.74 0.838 56 :1@N4_:2@C4 2982 0.399 4.39 0.85 57 :1@N4_:2@C5 2977 0.398 5.02 0.792 58 :1@C4_:2@O4 2970 0.397 4.44 0.851 59 :1@N1_:2@O2 2903 0.388 5.9 0.7 60 :1@N4_:2@O4 2895 0.387 4.48 0.896 61 :1@C6_:2@O4 2865 0.383 5.4 0.891 62 :1@C6_:2@O2 2863 0.383 5.65 0.781 63 :1@C5_:2@O4 2837 0.379 5.03 0.929 64 :1@O2_:2@O2 2740 0.366 5.69 0.957 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 7482, 'v_base2' size 7482, output size 7482 TIME: Analyses took 0.0009 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 7482 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 7482 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 7482 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 7482 COM "COM" (double, distance), size is 7482 v_base1 "v_base1" (vector, vector), size is 7482 v_base2 "v_base2" (vector, vector), size is 7482 normalangle "normalangle" (double), size is 7482 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.0906 s ( 98.66%) TIME: Action Post : 0.0002 s ( 0.22%) TIME: Analysis : 0.0009 s ( 1.03%) TIME: Data File Write : 0.0000 s ( 0.03%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0918 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: 0.1377 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.