CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:17:01 | Available memory: 1.974 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 :1@N1,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2' 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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,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 (1 total): 0: [traj] noWAt.topo.hmr, 59 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 58773 of 58773) Coordinate processing will occur on 58773 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 :1@N1,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 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 7 atoms. ----- ctraj.c3 (1-58773, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 56 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@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' 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@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@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' Atom ':1@O4' to ':2@N1' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' 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@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@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 58773 frames and processed 58773 frames. TIME: Avg. throughput= 154439.0080 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 26.1582 56 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 41113 0.7 5.59 0.982 2 :1@C2_:2@C6 38795 0.66 5.48 1.06 3 :1@C6_:2@C6 37847 0.644 5.6 0.983 4 :1@O2_:2@C6 36429 0.62 5.39 1.11 5 :1@N1_:2@N1 36150 0.615 5.77 0.795 6 :1@C6_:2@N1 35786 0.609 5.7 0.887 7 :1@C2_:2@N1 34220 0.582 5.55 0.882 8 :1@C5_:2@N1 33939 0.577 5.6 0.962 9 :1@N3_:2@C6 33617 0.572 5.48 0.989 10 :1@C5_:2@C6 33604 0.572 5.59 0.961 11 :1@C2_:2@C5 32719 0.557 5.12 1.22 12 :1@O2_:2@C5 32301 0.55 5.11 1.21 13 :1@N3_:2@N1 32262 0.549 5.5 0.908 14 :1@C4_:2@N1 31964 0.544 5.59 0.914 15 :1@N1_:2@C5 31888 0.543 5.22 1.1 16 :1@C4_:2@C6 31323 0.533 5.59 0.91 17 :1@C6_:2@C5 30244 0.515 5.33 1.12 18 :1@N3_:2@C5 29319 0.499 5.05 1.17 19 :1@C5_:2@C5 27611 0.47 5.25 1.11 20 :1@C5_:2@C2 27573 0.469 5.33 1.13 21 :1@C4_:2@C2 26883 0.457 5.16 1.13 22 :1@N3_:2@C2 26854 0.457 5.13 1.09 23 :1@O2_:2@C4 26724 0.455 5.04 1.1 24 :1@C2_:2@C2 26693 0.454 5.34 0.981 25 :1@O4_:2@N1 26674 0.454 5.71 0.855 26 :1@C4_:2@C5 26600 0.453 5.11 1.06 27 :1@C2_:2@C4 26326 0.448 4.91 1.07 28 :1@C6_:2@C2 25700 0.437 5.5 0.956 29 :1@N1_:2@C4 25587 0.435 5.24 0.905 30 :1@N3_:2@C4 25260 0.43 4.62 1.14 31 :1@O4_:2@C2 24775 0.422 5.19 1.09 32 :1@C4_:2@O2 24543 0.418 5.26 1.11 33 :1@N1_:2@C2 24430 0.416 5.54 0.814 34 :1@O4_:2@C6 24349 0.414 5.75 0.788 35 :1@C2_:2@N3 24229 0.412 5.01 0.962 36 :1@C2_:2@O4 24188 0.412 4.97 0.992 37 :1@O2_:2@O4 24038 0.409 5.07 1.06 38 :1@C4_:2@C4 24027 0.409 4.64 1.09 39 :1@N3_:2@N3 24007 0.408 4.65 1.11 40 :1@N3_:2@O4 23945 0.407 4.6 1.1 41 :1@C6_:2@C4 23926 0.407 5.2 0.948 42 :1@C5_:2@N3 23742 0.404 4.99 1.06 43 :1@C4_:2@N3 23715 0.404 4.66 1.13 44 :1@C5_:2@O2 23620 0.402 5.35 1.15 45 :1@C5_:2@C4 23596 0.401 4.91 1.05 46 :1@N1_:2@N3 23217 0.395 5.37 0.77 47 :1@O4_:2@C5 22904 0.39 5.26 0.888 48 :1@C6_:2@N3 22803 0.388 5.3 0.852 49 :1@O4_:2@N3 22753 0.387 4.67 1.14 50 :1@C4_:2@O4 22732 0.387 4.59 1.07 51 :1@N1_:2@O4 22631 0.385 5.36 0.832 52 :1@O4_:2@C4 22613 0.385 4.71 1.04 53 :1@O4_:2@O4 21870 0.372 4.56 1.07 54 :1@C5_:2@O4 21411 0.364 4.91 1.06 55 :1@C6_:2@O4 21119 0.359 5.29 0.935 56 :1@C6_:2@O2 20205 0.344 5.49 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 58773, 'v_base2' size 58773, output size 58773 TIME: Analyses took 0.0039 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 58773 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 58773 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 58773 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 58773 COM "COM" (double, distance), size is 58773 v_base1 "v_base1" (vector, vector), size is 58773 v_base2 "v_base2" (vector, vector), size is 58773 normalangle "normalangle" (double), size is 58773 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.3806 s ( 98.93%) TIME: Action Post : 0.0001 s ( 0.03%) TIME: Analysis : 0.0039 s ( 1.02%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.3847 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: 0.5751 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.