CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:03:03 | Available memory: 1.736 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.c3] Reading '../ctraj.c3' 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 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':1@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 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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] [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, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5593 of 5593) Coordinate processing will occur on 5593 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*](40) Reference mask: [:1,2&!@H*](40) 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 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [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. ----- ctraj.c3 (1-5593, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 88 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C4' Atom ':2@N9' to ':1@N4' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C4' Atom ':2@C8' to ':1@N4' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C4' Atom ':2@N7' to ':1@N4' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@N4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@O6' to ':1@N1' Atom ':2@O6' to ':1@C6' Atom ':2@O6' to ':1@C5' Atom ':2@O6' to ':1@C4' Atom ':2@O6' to ':1@N4' Atom ':2@O6' to ':1@N3' Atom ':2@O6' to ':1@C2' Atom ':2@O6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@N4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@N4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N2' to ':1@N1' Atom ':2@N2' to ':1@C6' Atom ':2@N2' to ':1@C5' Atom ':2@N2' to ':1@C4' Atom ':2@N2' to ':1@N4' Atom ':2@N2' to ':1@N3' Atom ':2@N2' to ':1@C2' Atom ':2@N2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@N4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@N4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 5593 frames and processed 5593 frames. TIME: Avg. throughput= 60217.4849 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 79.1818 88 # Contact Nframes Frac. Avg Stdev 1 :2@N2_:1@N1 5473 0.979 4.23 0.541 2 :2@N3_:1@N1 5454 0.975 4.35 0.561 3 :2@N2_:1@C2 5452 0.975 4.05 0.613 4 :2@N3_:1@C6 5434 0.972 4.17 0.652 5 :2@C2_:1@N1 5427 0.97 4.26 0.528 6 :2@N2_:1@O2 5424 0.97 4.18 0.699 7 :2@N2_:1@C6 5423 0.97 4.64 0.671 8 :2@C2_:1@C2 5394 0.964 4.09 0.617 9 :2@C2_:1@C6 5386 0.963 4.35 0.651 10 :2@N2_:1@N3 5384 0.963 4.33 0.634 11 :2@N3_:1@C2 5382 0.962 4.51 0.633 12 :2@N3_:1@C5 5356 0.958 4.16 0.638 13 :2@C2_:1@O2 5346 0.956 4.49 0.708 14 :2@C4_:1@C6 5345 0.956 4.47 0.611 15 :2@N1_:1@N1 5333 0.954 4.79 0.499 16 :2@C2_:1@N3 5331 0.953 4.05 0.625 17 :2@N2_:1@C4 5330 0.953 4.7 0.64 18 :2@C4_:1@N1 5329 0.953 4.94 0.527 19 :2@C2_:1@C5 5327 0.952 4.3 0.701 20 :2@N2_:1@C5 5327 0.952 4.86 0.704 21 :2@N3_:1@N3 5325 0.952 4.53 0.652 22 :2@N3_:1@C4 5315 0.95 4.36 0.586 23 :2@N1_:1@C2 5311 0.95 4.32 0.599 24 :2@C4_:1@C5 5308 0.949 4.12 0.656 25 :2@C2_:1@C4 5304 0.948 4.14 0.612 26 :2@N3_:1@O2 5288 0.945 5.08 0.703 27 :2@N1_:1@N3 5284 0.945 3.92 0.658 28 :2@N9_:1@C5 5276 0.943 4.55 0.668 29 :2@N9_:1@C6 5270 0.942 4.9 0.565 30 :2@N1_:1@C6 5268 0.942 4.82 0.628 31 :2@C4_:1@C4 5263 0.941 4.32 0.662 32 :2@N1_:1@C4 5258 0.94 3.97 0.667 33 :2@C4_:1@C2 5256 0.94 5.07 0.667 34 :2@N1_:1@O2 5254 0.939 4.7 0.724 35 :2@N1_:1@C5 5240 0.937 4.43 0.734 36 :2@C5_:1@C4 5233 0.936 4.2 0.678 37 :2@N9_:1@N1 5229 0.935 5.61 0.501 38 :2@C6_:1@C4 5223 0.934 4.02 0.626 39 :2@C6_:1@N3 5223 0.934 4.29 0.7 40 :2@C4_:1@N3 5223 0.934 4.78 0.733 41 :2@C2_:1@N4 5218 0.933 4.64 0.589 42 :2@C5_:1@C5 5217 0.933 4.29 0.61 43 :2@C5_:1@N1 5216 0.933 5.45 0.482 44 :2@N3_:1@N4 5213 0.932 4.89 0.543 45 :2@C6_:1@C2 5212 0.932 4.97 0.62 46 :2@C5_:1@C6 5206 0.931 4.95 0.525 47 :2@C6_:1@N1 5197 0.929 5.4 0.447 48 :2@C6_:1@C5 5196 0.929 4.48 0.65 49 :2@C5_:1@N4 5192 0.928 4.09 0.733 50 :2@C5_:1@N3 5192 0.928 4.72 0.767 51 :2@C4_:1@N4 5191 0.928 4.57 0.67 52 :2@C6_:1@N4 5190 0.928 3.85 0.68 53 :2@N1_:1@N4 5190 0.928 4.13 0.683 54 :2@C6_:1@C6 5185 0.927 5.16 0.543 55 :2@N9_:1@C4 5183 0.927 5 0.708 56 :2@C5_:1@C2 5157 0.922 5.31 0.658 57 :2@O6_:1@C4 5148 0.92 4.43 0.579 58 :2@N2_:1@N4 5147 0.92 5.35 0.609 59 :2@O6_:1@N4 5143 0.92 3.96 0.685 60 :2@O6_:1@N3 5143 0.92 4.66 0.639 61 :2@C8_:1@C5 5131 0.917 4.91 0.653 62 :2@N7_:1@C5 5127 0.917 4.82 0.615 63 :2@N7_:1@C4 5108 0.913 4.83 0.712 64 :2@N7_:1@N4 5096 0.911 4.49 0.826 65 :2@O6_:1@C5 5084 0.909 5.1 0.64 66 :2@C8_:1@C6 5058 0.904 5.54 0.545 67 :2@O6_:1@C2 5051 0.903 5.52 0.558 68 :2@N9_:1@N4 5040 0.901 5.15 0.74 69 :2@N7_:1@C6 5029 0.899 5.61 0.532 70 :2@C8_:1@C4 5010 0.896 5.19 0.731 71 :2@C6_:1@O2 5008 0.895 5.49 0.723 72 :2@C8_:1@N4 4951 0.885 5.04 0.832 73 :2@O6_:1@C6 4907 0.877 5.9 0.505 74 :2@O6_:1@N1 4905 0.877 6.12 0.4 75 :2@C4_:1@O2 4848 0.867 5.71 0.695 76 :2@N9_:1@N3 4835 0.864 5.56 0.697 77 :2@N7_:1@N3 4798 0.858 5.48 0.739 78 :2@N9_:1@C2 4761 0.851 5.84 0.599 79 :2@O6_:1@O2 4529 0.81 5.89 0.663 80 :2@N7_:1@N1 4464 0.798 6.22 0.454 81 :2@C5_:1@O2 4450 0.796 5.88 0.668 82 :2@C8_:1@N1 4406 0.788 6.24 0.447 83 :2@C8_:1@N3 4352 0.778 5.81 0.684 84 :2@N7_:1@C2 4187 0.749 6.07 0.567 85 :2@C8_:1@C2 3632 0.649 6.23 0.527 86 :2@N9_:1@O2 2955 0.528 6.27 0.61 87 :2@N7_:1@O2 2072 0.37 6.34 0.539 88 :2@C8_:1@O2 1326 0.237 6.38 0.566 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 5593, 'v_base2' size 5593, output size 5593 TIME: Analyses took 0.0008 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 5593 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 5593 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 5593 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 5593 COM "COM" (double, distance), size is 5593 v_base2 "v_base2" (vector, vector), size is 5593 v_base1 "v_base1" (vector, vector), size is 5593 normalangle "normalangle" (double), size is 5593 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.0929 s ( 98.82%) TIME: Action Post : 0.0003 s ( 0.28%) TIME: Analysis : 0.0008 s ( 0.81%) TIME: Data File Write : 0.0000 s ( 0.03%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0940 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: 0.1297 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.