CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 11:32:29 | Available memory: 1.218 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.c4] Reading '../ctraj.c4' 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.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56363 of 56363) Coordinate processing will occur on 56363 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.c4 (1-56363, 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 56363 frames and processed 56363 frames. TIME: Avg. throughput= 152399.9827 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 26.3127 56 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 38894 0.69 5.56 0.989 2 :1@C2_:2@C6 37456 0.665 5.45 1.06 3 :1@C6_:2@C6 35904 0.637 5.6 0.985 4 :1@O2_:2@C6 35445 0.629 5.38 1.11 5 :1@N1_:2@N1 35054 0.622 5.75 0.792 6 :1@C6_:2@N1 34361 0.61 5.68 0.891 7 :1@C2_:2@N1 33684 0.598 5.55 0.884 8 :1@C5_:2@N1 32878 0.583 5.58 0.964 9 :1@N3_:2@C6 32841 0.583 5.47 0.989 10 :1@C5_:2@C6 32180 0.571 5.59 0.965 11 :1@N3_:2@N1 31898 0.566 5.49 0.908 12 :1@C4_:2@N1 31704 0.562 5.59 0.913 13 :1@C2_:2@C5 30914 0.548 5.07 1.22 14 :1@O2_:2@C5 30813 0.547 5.08 1.2 15 :1@C4_:2@C6 30325 0.538 5.57 0.912 16 :1@N1_:2@C5 29795 0.529 5.18 1.11 17 :1@C6_:2@C5 28299 0.502 5.33 1.11 18 :1@N3_:2@C5 28072 0.498 5.01 1.17 19 :1@C4_:2@C2 26674 0.473 5.16 1.13 20 :1@C5_:2@C2 26638 0.473 5.3 1.12 21 :1@N3_:2@C2 26590 0.472 5.12 1.09 22 :1@O4_:2@N1 26542 0.471 5.71 0.855 23 :1@C2_:2@C2 26313 0.467 5.33 0.981 24 :1@C5_:2@C5 26014 0.462 5.25 1.1 25 :1@O2_:2@C4 25908 0.46 5.02 1.09 26 :1@C4_:2@C5 25339 0.45 5.08 1.06 27 :1@C2_:2@C4 25202 0.447 4.85 1.04 28 :1@C6_:2@C2 24636 0.437 5.47 0.953 29 :1@O4_:2@C2 24619 0.437 5.19 1.09 30 :1@C4_:2@O2 24379 0.433 5.25 1.11 31 :1@N3_:2@C4 24348 0.432 4.57 1.12 32 :1@N1_:2@C4 24213 0.43 5.2 0.9 33 :1@N1_:2@C2 23973 0.425 5.52 0.81 34 :1@O4_:2@C6 23805 0.422 5.73 0.786 35 :1@C2_:2@N3 23804 0.422 4.99 0.955 36 :1@N3_:2@N3 23708 0.421 4.64 1.1 37 :1@C5_:2@O2 23316 0.414 5.34 1.15 38 :1@O2_:2@O4 23217 0.412 5.03 1.06 39 :1@C2_:2@O4 23065 0.409 4.91 0.97 40 :1@C4_:2@N3 23036 0.409 4.62 1.11 41 :1@C4_:2@C4 22961 0.407 4.59 1.08 42 :1@N3_:2@O4 22915 0.407 4.54 1.07 43 :1@C5_:2@N3 22635 0.402 4.95 1.05 44 :1@C6_:2@C4 22578 0.401 5.19 0.943 45 :1@N1_:2@N3 22489 0.399 5.35 0.757 46 :1@O4_:2@N3 22311 0.396 4.64 1.12 47 :1@C5_:2@C4 22277 0.395 4.89 1.04 48 :1@O4_:2@C5 21896 0.388 5.23 0.886 49 :1@C6_:2@N3 21705 0.385 5.27 0.847 50 :1@O4_:2@C4 21665 0.384 4.66 1.02 51 :1@C4_:2@O4 21624 0.384 4.55 1.07 52 :1@N1_:2@O4 21412 0.38 5.33 0.827 53 :1@O4_:2@O4 20817 0.369 4.52 1.06 54 :1@C5_:2@O4 20178 0.358 4.91 1.05 55 :1@C6_:2@O4 19913 0.353 5.3 0.928 56 :1@C6_:2@O2 19828 0.352 5.48 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 56363, 'v_base2' size 56363, output size 56363 TIME: Analyses took 0.0038 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 56363 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 56363 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 56363 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 56363 COM "COM" (double, distance), size is 56363 v_base1 "v_base1" (vector, vector), size is 56363 v_base2 "v_base2" (vector, vector), size is 56363 normalangle "normalangle" (double), size is 56363 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.3698 s ( 98.94%) TIME: Action Post : 0.0001 s ( 0.03%) TIME: Analysis : 0.0038 s ( 1.01%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.3738 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: 0.5258 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.