CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:06:13 | Available memory: 1.228 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.c2] Reading '../ctraj.c2' 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,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [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, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8517 of 8517) Coordinate processing will occur on 8517 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,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 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.c2 (1-8517, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 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@N1' 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@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@N4' to ':2@N1' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' 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@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@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 8517 frames and processed 8517 frames. TIME: Avg. throughput= 80129.0796 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 33.6738 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 6215 0.73 5.26 0.997 2 :1@C2_:2@C6 5853 0.687 5.15 1.03 3 :1@O2_:2@C6 5751 0.675 5.1 0.991 4 :1@C6_:2@C6 5657 0.664 5.31 1.02 5 :1@O2_:2@C5 5599 0.657 4.8 1.08 6 :1@N1_:2@C5 5537 0.65 4.97 0.993 7 :1@N1_:2@N1 5511 0.647 5.54 0.809 8 :1@C2_:2@C5 5485 0.644 4.78 1.09 9 :1@O2_:2@N1 5290 0.621 5.43 0.924 10 :1@C2_:2@N1 5276 0.619 5.38 0.872 11 :1@C6_:2@C5 5081 0.597 5.13 1.04 12 :1@C6_:2@N1 4997 0.587 5.39 0.92 13 :1@O2_:2@C4 4966 0.583 4.84 1.02 14 :1@N3_:2@C6 4952 0.581 5.14 0.954 15 :1@N3_:2@C5 4938 0.58 4.78 1.08 16 :1@C2_:2@C4 4859 0.571 4.75 0.966 17 :1@C5_:2@C6 4850 0.569 5.25 0.991 18 :1@N1_:2@C4 4815 0.565 5.13 0.834 19 :1@C2_:2@O4 4681 0.55 4.89 0.906 20 :1@O2_:2@O4 4653 0.546 4.88 1 21 :1@N3_:2@N1 4625 0.543 5.26 0.947 22 :1@N3_:2@C4 4608 0.541 4.52 1.12 23 :1@C5_:2@N1 4598 0.54 5.22 0.996 24 :1@O2_:2@C2 4590 0.539 5.42 1.02 25 :1@C4_:2@C6 4586 0.538 5.22 0.942 26 :1@O2_:2@N3 4575 0.537 5.14 1.06 27 :1@C5_:2@C5 4531 0.532 5.03 1.02 28 :1@C4_:2@C5 4502 0.529 4.88 1.02 29 :1@N3_:2@O4 4473 0.525 4.56 1.03 30 :1@N1_:2@O4 4456 0.523 5.34 0.768 31 :1@C2_:2@C2 4441 0.521 5.25 0.94 32 :1@C2_:2@N3 4428 0.52 4.95 0.998 33 :1@C6_:2@C4 4327 0.508 5.13 0.903 34 :1@C4_:2@N1 4323 0.508 5.17 0.93 35 :1@C6_:2@C2 4320 0.507 5.39 0.834 36 :1@N1_:2@C2 4290 0.504 5.47 0.741 37 :1@N1_:2@N3 4256 0.5 5.29 0.768 38 :1@C5_:2@C2 4239 0.498 5.06 1.02 39 :1@C4_:2@C4 4222 0.496 4.53 1.05 40 :1@N3_:2@N3 4171 0.49 4.5 1.06 41 :1@N3_:2@C2 4170 0.49 4.89 0.994 42 :1@C4_:2@O4 4167 0.489 4.64 1.02 43 :1@C6_:2@N3 4156 0.488 5.26 0.783 44 :1@C4_:2@C2 4154 0.488 4.85 1.05 45 :1@C4_:2@N3 4119 0.484 4.51 1.06 46 :1@C5_:2@N3 4115 0.483 4.88 0.954 47 :1@C5_:2@C4 4059 0.477 4.8 0.946 48 :1@C6_:2@O4 4029 0.473 5.37 0.944 49 :1@C4_:2@O2 3918 0.46 5.08 0.958 50 :1@N4_:2@C5 3903 0.458 5.13 0.856 51 :1@C5_:2@O2 3902 0.458 5.28 0.973 52 :1@C5_:2@O4 3886 0.456 4.99 1.01 53 :1@N4_:2@N3 3874 0.455 4.43 1.1 54 :1@N3_:2@O2 3860 0.453 5.21 0.946 55 :1@N4_:2@O4 3849 0.452 4.58 1 56 :1@N4_:2@C4 3846 0.452 4.55 0.953 57 :1@N4_:2@N1 3827 0.449 5.33 0.85 58 :1@N4_:2@C2 3819 0.448 4.79 1.02 59 :1@N4_:2@C6 3787 0.445 5.48 0.775 60 :1@N4_:2@O2 3763 0.442 4.92 1.03 61 :1@C6_:2@O2 3712 0.436 5.68 0.812 62 :1@C2_:2@O2 3638 0.427 5.54 0.923 63 :1@N1_:2@O2 3490 0.41 5.81 0.794 64 :1@O2_:2@O2 3230 0.379 5.56 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 8517, 'v_base2' size 8517, output size 8517 TIME: Analyses took 0.0011 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 8517 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8517 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8517 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8517 COM "COM" (double, distance), size is 8517 v_base1 "v_base1" (vector, vector), size is 8517 v_base2 "v_base2" (vector, vector), size is 8517 normalangle "normalangle" (double), size is 8517 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.1063 s ( 98.72%) TIME: Action Post : 0.0002 s ( 0.20%) TIME: Analysis : 0.0011 s ( 1.00%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1077 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: 0.1567 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.