CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 12:00:57 | Available memory: 1.219 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 54936 of 54936) Coordinate processing will occur on 54936 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-54936, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 40 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' 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@O4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' 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@O4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@O4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' Atom ':2@N4' to ':1@N1' Atom ':2@N4' to ':1@C4' Atom ':2@N4' to ':1@O4' Atom ':2@N4' to ':1@N3' Atom ':2@N4' to ':1@C2' Atom ':2@N4' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 54936 frames and processed 54936 frames. TIME: Avg. throughput= 126884.4076 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 38.4798 40 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 54592 0.994 4.56 0.559 2 :2@C5_:1@N1 54564 0.993 4.35 0.502 3 :2@C5_:1@C2 54493 0.992 4.34 0.623 4 :2@C6_:1@C2 54451 0.991 4.61 0.641 5 :2@C6_:1@O2 54293 0.988 4.76 0.753 6 :2@C4_:1@C2 54262 0.988 4.39 0.694 7 :2@C4_:1@N1 54162 0.986 4.67 0.604 8 :2@C5_:1@N3 54151 0.986 4.48 0.68 9 :2@C5_:1@O2 54146 0.986 4.68 0.874 10 :2@N1_:1@N1 54071 0.984 5.05 0.605 11 :2@C5_:1@C6 54013 0.983 4.44 0.764 12 :2@N1_:1@O2 53991 0.983 4.83 0.786 13 :2@N1_:1@C2 53977 0.983 4.89 0.737 14 :2@C4_:1@N3 53837 0.98 4.24 0.712 15 :2@C6_:1@C6 53778 0.979 4.89 0.794 16 :2@N4_:1@N3 53732 0.978 4.21 0.898 17 :2@N4_:1@C2 53608 0.976 4.65 0.892 18 :2@C6_:1@N3 53603 0.976 5 0.76 19 :2@N4_:1@N1 53598 0.976 5 0.724 20 :2@N3_:1@C2 53495 0.974 4.66 0.737 21 :2@C5_:1@C4 53479 0.973 4.62 0.74 22 :2@C4_:1@O2 53301 0.97 4.67 0.938 23 :2@C2_:1@O2 53290 0.97 4.82 0.84 24 :2@N3_:1@O2 53070 0.966 4.76 0.934 25 :2@C5_:1@C5 53029 0.965 4.53 0.855 26 :2@C2_:1@C2 53018 0.965 4.88 0.723 27 :2@N4_:1@C4 52949 0.964 4.08 0.778 28 :2@C4_:1@C4 52741 0.96 4.32 0.766 29 :2@N3_:1@N1 52661 0.959 5.07 0.683 30 :2@C4_:1@C6 52645 0.958 4.69 0.757 31 :2@N3_:1@N3 52572 0.957 4.5 0.799 32 :2@N4_:1@O4 52242 0.951 4.18 0.837 33 :2@C5_:1@O4 51581 0.939 5.16 0.754 34 :2@C6_:1@C5 51498 0.937 5.19 0.886 35 :2@C6_:1@C4 51449 0.937 5.3 0.83 36 :2@N1_:1@N3 51383 0.935 5.2 0.924 37 :2@C4_:1@O4 51380 0.935 4.65 0.839 38 :2@O2_:1@O2 49627 0.903 5.17 0.869 39 :2@N4_:1@O2 48731 0.887 4.88 1 40 :2@C6_:1@O4 42464 0.773 5.76 0.742 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 54936, 'v_base2' size 54936, output size 54936 TIME: Analyses took 0.0039 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 54936 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 54936 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 54936 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 54936 COM "COM" (double, distance), size is 54936 v_base1 "v_base1" (vector, vector), size is 54936 v_base2 "v_base2" (vector, vector), size is 54936 normalangle "normalangle" (double), size is 54936 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.4330 s ( 99.06%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0039 s ( 0.90%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4371 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: 0.5865 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.