CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 11:57:08 | Available memory: 1.747 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.c1] Reading '../ctraj.c1' 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,O4,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,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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,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,O4,N3,H3,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,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, 62 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 15903 of 15903) Coordinate processing will occur on 15903 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,O4,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,O4,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,O4,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,O4,N3,H3,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,O4,N3,H3,C2,O2 (11 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,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-15903, 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,O4,N3,C2,O2] corresponds to 8 atoms. Setup 78 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@O4' 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@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@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@O4' 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@O4' 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@O4' 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@O4' 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@O4' 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@O4' 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@O4' 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 15903 frames and processed 15903 frames. TIME: Avg. throughput= 64359.0802 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 74.1055 78 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 15892 0.999 4.24 0.614 2 :1@C4_:2@C5 15866 0.998 3.99 0.608 3 :1@N9_:2@C6 15850 0.997 4.7 0.556 4 :1@C4_:2@C6 15842 0.996 4.26 0.565 5 :1@N9_:2@C5 15839 0.996 4.33 0.63 6 :1@N3_:2@C6 15825 0.995 3.99 0.589 7 :1@N3_:2@C5 15825 0.995 4.06 0.595 8 :1@N3_:2@C4 15820 0.995 4.4 0.577 9 :1@C5_:2@C4 15819 0.995 4.07 0.762 10 :1@N3_:2@N1 15805 0.994 4.23 0.529 11 :1@N3_:2@N3 15799 0.993 4.57 0.602 12 :1@N3_:2@C2 15792 0.993 4.53 0.588 13 :1@C5_:2@C5 15789 0.993 4.23 0.742 14 :1@C4_:2@N1 15782 0.992 4.72 0.515 15 :1@C4_:2@O4 15776 0.992 4.57 0.657 16 :1@C2_:2@C6 15756 0.991 4.22 0.693 17 :1@C4_:2@N3 15756 0.991 4.64 0.641 18 :1@C2_:2@C2 15748 0.99 4.08 0.67 19 :1@C2_:2@N3 15741 0.99 4.16 0.674 20 :1@C6_:2@C4 15731 0.989 4.03 0.743 21 :1@C2_:2@C5 15729 0.989 4.31 0.725 22 :1@C2_:2@N1 15728 0.989 4.1 0.629 23 :1@N1_:2@N3 15724 0.989 3.93 0.701 24 :1@C2_:2@C4 15712 0.988 4.31 0.694 25 :1@C6_:2@N3 15696 0.987 4.05 0.732 26 :1@N3_:2@O4 15689 0.987 4.98 0.639 27 :1@N1_:2@C4 15682 0.986 4.17 0.731 28 :1@C4_:2@C2 15665 0.985 4.9 0.604 29 :1@C6_:2@O4 15660 0.985 4.14 0.815 30 :1@N1_:2@C2 15653 0.984 4.09 0.666 31 :1@C5_:2@O4 15648 0.984 4.12 0.8 32 :1@C6_:2@C5 15642 0.984 4.5 0.743 33 :1@N9_:2@C4 15629 0.983 4.75 0.672 34 :1@C5_:2@C6 15611 0.982 4.74 0.624 35 :1@N9_:2@N1 15599 0.981 5.4 0.524 36 :1@C5_:2@N3 15594 0.981 4.42 0.741 37 :1@N1_:2@C5 15594 0.981 4.54 0.745 38 :1@C2_:2@O2 15560 0.978 4.49 0.733 39 :1@N1_:2@C6 15557 0.978 4.69 0.663 40 :1@N1_:2@N1 15511 0.975 4.47 0.563 41 :1@C8_:2@C5 15505 0.975 4.68 0.76 42 :1@N3_:2@O2 15468 0.973 5.16 0.652 43 :1@C6_:2@C6 15448 0.971 4.91 0.621 44 :1@N1_:2@O4 15439 0.971 4.51 0.773 45 :1@N6_:2@C4 15427 0.97 4.42 0.8 46 :1@N7_:2@C5 15408 0.969 4.67 0.784 47 :1@C2_:2@O4 15403 0.969 4.85 0.749 48 :1@C6_:2@C2 15388 0.968 4.48 0.633 49 :1@N1_:2@O2 15362 0.966 4.36 0.704 50 :1@N6_:2@O4 15351 0.965 4.28 0.898 51 :1@C6_:2@N1 15344 0.965 4.91 0.539 52 :1@C5_:2@N1 15332 0.964 5.05 0.557 53 :1@N6_:2@N3 15294 0.962 4.3 0.735 54 :1@C8_:2@C6 15218 0.957 5.3 0.622 55 :1@C5_:2@C2 15212 0.957 4.89 0.654 56 :1@N9_:2@O4 15211 0.956 4.92 0.677 57 :1@N7_:2@C4 15186 0.955 4.46 0.815 58 :1@N9_:2@N3 15126 0.951 5.37 0.671 59 :1@C8_:2@C4 15043 0.946 4.8 0.786 60 :1@N6_:2@C2 15020 0.944 4.9 0.664 61 :1@C6_:2@O2 14958 0.941 4.88 0.708 62 :1@N7_:2@C6 14946 0.94 5.35 0.621 63 :1@N9_:2@C2 14938 0.939 5.7 0.604 64 :1@N6_:2@C5 14912 0.938 5.14 0.699 65 :1@C4_:2@O2 14858 0.934 5.59 0.649 66 :1@N6_:2@N1 14725 0.926 5.58 0.572 67 :1@N7_:2@N3 14665 0.922 5.01 0.801 68 :1@N6_:2@O2 14618 0.919 5.13 0.778 69 :1@N6_:2@C6 14553 0.915 5.67 0.579 70 :1@C5_:2@O2 14476 0.91 5.5 0.74 71 :1@C8_:2@N3 14211 0.894 5.48 0.781 72 :1@N7_:2@N1 14139 0.889 5.8 0.631 73 :1@C8_:2@N1 14079 0.885 5.93 0.598 74 :1@N7_:2@C2 14007 0.881 5.65 0.747 75 :1@C8_:2@C2 13090 0.823 5.99 0.704 76 :1@N9_:2@O2 10446 0.657 6.29 0.633 77 :1@N7_:2@O2 10017 0.63 6.06 0.843 78 :1@C8_:2@O2 5740 0.361 6.14 0.791 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 15903, 'v_base2' size 15903, output size 15903 TIME: Analyses took 0.0022 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 15903 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 15903 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 15903 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 15903 COM "COM" (double, distance), size is 15903 v_base1 "v_base1" (vector, vector), size is 15903 v_base2 "v_base2" (vector, vector), size is 15903 normalangle "normalangle" (double), size is 15903 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.2471 s ( 99.00%) TIME: Action Post : 0.0002 s ( 0.10%) TIME: Analysis : 0.0022 s ( 0.87%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2496 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: 0.3290 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.