CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 18:09:55 | Available memory: 52492.9 MB INPUT: Reading Input from file 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-] 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*), with fitting. [nativecontacts :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,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,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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,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: 0: [traj] 'noWAt.topo.hmr', 61 atoms, 2 res, box: Orthogonal, 1 mol, 55410 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 55410 of 55410) Coordinate processing will occur on 55410 frames. TIME: Run Initialization took 0.0002 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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,N4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c3 (1-55410, 1) ----- 0% 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,N4,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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 55410 frames and processed 55410 frames. TIME: Trajectory processing: 0.2691 s TIME: Avg. throughput= 205935.3688 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 47.4939 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 49642 0.896 5.02 0.909 2 :1@N1_:2@N1 48122 0.868 5.42 0.723 3 :1@C2_:2@C6 48089 0.868 4.87 1.03 4 :1@C6_:2@C6 47956 0.865 5.16 0.899 5 :1@C6_:2@N1 47827 0.863 5.42 0.823 6 :1@C5_:2@N1 46642 0.842 5.31 0.9 7 :1@C2_:2@N1 46098 0.832 5.16 0.889 8 :1@C4_:2@N1 45663 0.824 5.19 0.867 9 :1@N3_:2@C6 45443 0.82 4.93 0.976 10 :1@C5_:2@C6 45272 0.817 5.2 0.887 11 :1@O2_:2@C6 45160 0.815 4.89 1.07 12 :1@N3_:2@N1 45062 0.813 5.07 0.93 13 :1@C2_:2@C5 44854 0.809 4.53 1.04 14 :1@C4_:2@C6 44546 0.804 5.12 0.875 15 :1@N1_:2@C5 44175 0.797 4.72 0.894 16 :1@O2_:2@C5 43953 0.793 4.63 1.08 17 :1@N3_:2@C5 43202 0.78 4.54 1.04 18 :1@C4_:2@C2 42895 0.774 4.89 0.966 19 :1@C6_:2@C5 42686 0.77 4.91 0.946 20 :1@C5_:2@C2 42463 0.766 5.16 0.974 21 :1@N3_:2@C2 42176 0.761 4.85 0.983 22 :1@C2_:2@C4 41820 0.755 4.61 0.861 23 :1@N4_:2@N1 41753 0.754 5.42 0.822 24 :1@O2_:2@N1 41703 0.753 5.19 1 25 :1@C2_:2@C2 41504 0.749 5.16 0.857 26 :1@O2_:2@C4 41478 0.749 4.84 0.981 27 :1@C4_:2@C5 41364 0.747 4.71 0.944 28 :1@N4_:2@C2 41135 0.742 4.93 0.97 29 :1@N3_:2@C4 41124 0.742 4.32 0.954 30 :1@C5_:2@C5 40914 0.738 4.88 0.952 31 :1@N1_:2@C4 40840 0.737 4.99 0.712 32 :1@N1_:2@C2 40783 0.736 5.51 0.682 33 :1@N3_:2@N3 40666 0.734 4.5 0.948 34 :1@C6_:2@C2 40660 0.734 5.44 0.834 35 :1@C4_:2@O2 40634 0.733 5.21 0.932 36 :1@C2_:2@N3 40540 0.732 4.95 0.82 37 :1@C4_:2@N3 40056 0.723 4.48 0.923 38 :1@N4_:2@O2 40010 0.722 5.1 0.998 39 :1@C4_:2@C4 39854 0.719 4.37 0.922 40 :1@C2_:2@N4 39822 0.719 4.81 0.782 41 :1@N3_:2@N4 39590 0.714 4.43 0.898 42 :1@C6_:2@C4 39389 0.711 5.01 0.878 43 :1@N4_:2@C6 39349 0.71 5.48 0.756 44 :1@N1_:2@N3 39313 0.709 5.37 0.674 45 :1@N4_:2@N3 39257 0.708 4.47 0.968 46 :1@O2_:2@N4 39176 0.707 4.98 0.98 47 :1@C5_:2@N3 39054 0.705 4.87 0.956 48 :1@N3_:2@O2 38914 0.702 5.2 0.921 49 :1@O2_:2@N3 38902 0.702 5.18 0.89 50 :1@C5_:2@C4 38878 0.702 4.71 0.965 51 :1@N1_:2@N4 38748 0.699 5.28 0.712 52 :1@C5_:2@O2 38428 0.694 5.42 0.944 53 :1@C6_:2@N3 38421 0.693 5.29 0.846 54 :1@N4_:2@C4 38384 0.693 4.52 0.922 55 :1@O2_:2@C2 38188 0.689 5.29 0.923 56 :1@C4_:2@N4 38144 0.688 4.45 0.95 57 :1@N4_:2@C5 38112 0.688 5.06 0.845 58 :1@N4_:2@N4 36720 0.663 4.45 0.992 59 :1@C2_:2@O2 36085 0.651 5.58 0.838 60 :1@C6_:2@N4 36006 0.65 5.21 0.953 61 :1@C5_:2@N4 35925 0.648 4.79 1.05 62 :1@C6_:2@O2 34109 0.616 5.76 0.855 63 :1@N1_:2@O2 33617 0.607 5.96 0.785 64 :1@O2_:2@O2 30343 0.548 5.57 0.862 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0029 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 55410 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 55410 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 55410 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 55410 COM "COM" (double, distance), size is 55410 v_base1 "v_base1" (vector), size is 55410 v_base2 "v_base2" (vector), size is 55410 normalangle "normalangle" (double), size is 55410 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.3930 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.