CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/05/16 18:45:44 | Available memory: 1.945 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,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,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 :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,H41,H42,N3,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,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, 63 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 226863 of 226863) Coordinate processing will occur on 226863 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,N4,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,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-226863, 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,N4,N3,C2,O2] corresponds to 8 atoms. Setup 80 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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 226863 frames and processed 226863 frames. TIME: Avg. throughput= 71399.2122 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 77.7553 80 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N1 226726 0.999 4.22 0.438 2 :1@C4_:2@C6 226713 0.999 3.92 0.502 3 :1@N9_:2@C6 226657 0.999 4.17 0.439 4 :1@C5_:2@N1 226488 0.998 4.28 0.548 5 :1@N9_:2@N1 226373 0.998 4.76 0.457 6 :1@C4_:2@C5 226323 0.998 4.09 0.617 7 :1@C6_:2@N1 226239 0.997 4.32 0.588 8 :1@C5_:2@C6 226218 0.997 4.05 0.513 9 :1@C4_:2@C2 226067 0.996 4.67 0.487 10 :1@N9_:2@C5 225922 0.996 4.3 0.552 11 :1@C6_:2@C2 225885 0.996 4.08 0.569 12 :1@C5_:2@C2 225544 0.994 4.39 0.563 13 :1@C6_:2@C6 225442 0.994 4.42 0.607 14 :1@C5_:2@C5 225440 0.994 3.9 0.64 15 :1@C4_:2@C4 225291 0.993 4.56 0.604 16 :1@N3_:2@C6 225252 0.993 4.16 0.689 17 :1@N3_:2@N1 225200 0.993 4.2 0.624 18 :1@C4_:2@N3 225192 0.993 4.84 0.55 19 :1@C6_:2@N3 225049 0.992 3.95 0.597 20 :1@C6_:2@O2 224911 0.991 4.5 0.686 21 :1@C5_:2@N3 224899 0.991 4.3 0.545 22 :1@C5_:2@C4 224898 0.991 4.03 0.623 23 :1@C8_:2@C6 224795 0.991 4.38 0.589 24 :1@N6_:2@C2 224608 0.99 4.34 0.669 25 :1@N7_:2@C6 224354 0.989 4.36 0.585 26 :1@N1_:2@C2 224323 0.989 4.04 0.675 27 :1@N9_:2@C4 224288 0.989 5.03 0.56 28 :1@N6_:2@N3 224286 0.989 3.98 0.623 29 :1@C6_:2@C4 224260 0.989 4.01 0.728 30 :1@C6_:2@C5 224210 0.988 4.27 0.729 31 :1@N9_:2@C2 224196 0.988 5.41 0.517 32 :1@N7_:2@N1 224060 0.988 4.83 0.775 33 :1@C8_:2@N1 224053 0.988 5.05 0.723 34 :1@N6_:2@N1 223992 0.987 4.9 0.652 35 :1@N3_:2@C2 223954 0.987 4.68 0.644 36 :1@N1_:2@N1 223825 0.987 4.26 0.659 37 :1@C5_:2@O2 223736 0.986 5.05 0.697 38 :1@C4_:2@O2 223707 0.986 5.35 0.538 39 :1@C8_:2@C5 223459 0.985 4.18 0.694 40 :1@N6_:2@O2 223280 0.984 4.61 0.87 41 :1@N7_:2@C5 223279 0.984 3.98 0.694 42 :1@N1_:2@O2 223214 0.984 4.27 0.697 43 :1@N1_:2@N3 223205 0.984 4.17 0.787 44 :1@N3_:2@C5 223166 0.984 4.56 0.762 45 :1@N1_:2@C6 223033 0.983 4.6 0.712 46 :1@C2_:2@N1 222967 0.983 4.15 0.715 47 :1@N6_:2@C4 222885 0.982 4.15 0.75 48 :1@N7_:2@C2 222770 0.982 4.99 0.844 49 :1@N9_:2@N3 222763 0.982 5.53 0.541 50 :1@C2_:2@C6 222715 0.982 4.42 0.766 51 :1@N6_:2@C6 222682 0.982 5.09 0.593 52 :1@C2_:2@C2 222606 0.981 4.29 0.748 53 :1@N7_:2@N3 222469 0.981 4.72 0.761 54 :1@C5_:2@N4 222165 0.979 4.48 0.773 55 :1@N7_:2@C4 221869 0.978 4.19 0.726 56 :1@N6_:2@C5 221536 0.977 4.74 0.722 57 :1@N3_:2@N3 221215 0.975 5.06 0.699 58 :1@N3_:2@O2 220563 0.972 5.18 0.646 59 :1@C4_:2@N4 220311 0.971 5.2 0.671 60 :1@C2_:2@O2 220293 0.971 4.57 0.752 61 :1@C6_:2@N4 220130 0.97 4.4 0.876 62 :1@C8_:2@C4 220040 0.97 4.74 0.705 63 :1@N1_:2@C4 219277 0.967 4.41 0.844 64 :1@C2_:2@N3 219228 0.966 4.64 0.814 65 :1@N1_:2@C5 219227 0.966 4.66 0.8 66 :1@C8_:2@C2 219080 0.966 5.5 0.759 67 :1@N3_:2@C4 218866 0.965 4.96 0.731 68 :1@C8_:2@N3 218494 0.963 5.38 0.718 69 :1@N6_:2@N4 218488 0.963 4.25 0.953 70 :1@C2_:2@C5 216848 0.956 4.71 0.825 71 :1@N9_:2@N4 215559 0.95 5.58 0.594 72 :1@N7_:2@N4 214527 0.946 4.34 0.757 73 :1@C2_:2@C4 213046 0.939 4.75 0.824 74 :1@C8_:2@N4 209787 0.925 5.01 0.683 75 :1@N1_:2@N4 204036 0.899 4.83 0.832 76 :1@N7_:2@O2 200125 0.882 5.62 0.934 77 :1@N9_:2@O2 199568 0.88 6.11 0.516 78 :1@N3_:2@N4 196257 0.865 5.58 0.683 79 :1@C2_:2@N4 192545 0.849 5.3 0.817 80 :1@C8_:2@O2 158847 0.7 6 0.746 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 226863, 'v_base2' size 226863, output size 226863 TIME: Analyses took 0.0331 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 226863 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 226863 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 226863 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 226863 COM "COM" (double, distance), size is 226863 v_base1 "v_base1" (vector, vector), size is 226863 v_base2 "v_base2" (vector, vector), size is 226863 normalangle "normalangle" (double), size is 226863 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0027 s ( 0.08%) TIME: Trajectory Process : 3.1774 s ( 98.88%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0331 s ( 1.03%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 3.2135 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: 3.9250 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.