CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:18:50 | Available memory: 7.242 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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 52498 of 52498) Coordinate processing will occur on 52498 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.c0 (1-52498, 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 52498 frames and processed 52498 frames. TIME: Avg. throughput= 68939.9779 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 63.0415 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@N1 52488 1 4.46 0.346 2 :1@N1_:2@C6 52487 1 4.14 0.375 3 :1@N1_:2@C5 52479 1 4.34 0.439 4 :1@C6_:2@C6 52478 1 4.04 0.393 5 :1@C6_:2@N1 52471 0.999 4.55 0.46 6 :1@C6_:2@C5 52465 0.999 3.83 0.388 7 :1@C2_:2@N1 52449 0.999 4.27 0.504 8 :1@C6_:2@C4 52447 0.999 4.21 0.433 9 :1@C5_:2@N3 52437 0.999 3.99 0.5 10 :1@C5_:2@C2 52435 0.999 4.4 0.593 11 :1@C6_:2@N3 52431 0.999 4.67 0.506 12 :1@C5_:2@N1 52430 0.999 4.47 0.545 13 :1@N1_:2@C2 52430 0.999 4.95 0.421 14 :1@C5_:2@C6 52427 0.999 4.16 0.453 15 :1@C5_:2@C5 52426 0.999 3.74 0.423 16 :1@C6_:2@C2 52426 0.999 4.86 0.525 17 :1@C4_:2@C2 52424 0.999 3.98 0.486 18 :1@C4_:2@N1 52422 0.999 4.27 0.5 19 :1@C5_:2@C4 52421 0.999 3.66 0.397 20 :1@C2_:2@C6 52421 0.999 4.36 0.551 21 :1@N1_:2@C4 52403 0.998 4.88 0.46 22 :1@C4_:2@N3 52401 0.998 3.78 0.449 23 :1@N3_:2@N1 52395 0.998 4.18 0.541 24 :1@N1_:2@N3 52395 0.998 5.1 0.466 25 :1@C6_:2@O4 52374 0.998 4.63 0.523 26 :1@N3_:2@C2 52366 0.997 4.07 0.549 27 :1@N4_:2@C2 52356 0.997 4.08 0.583 28 :1@N4_:2@N3 52349 0.997 3.71 0.515 29 :1@C5_:2@O4 52349 0.997 3.92 0.507 30 :1@C4_:2@C4 52345 0.997 3.9 0.524 31 :1@C4_:2@C6 52344 0.997 4.37 0.487 32 :1@C2_:2@C2 52338 0.997 4.57 0.536 33 :1@C4_:2@C5 52318 0.997 4.18 0.543 34 :1@N3_:2@N3 52296 0.996 4.26 0.626 35 :1@C2_:2@C5 52296 0.996 4.73 0.596 36 :1@N3_:2@C6 52293 0.996 4.47 0.575 37 :1@C4_:2@O2 52276 0.996 4.43 0.632 38 :1@N4_:2@C4 52240 0.995 4.03 0.611 39 :1@N4_:2@N1 52196 0.994 4.74 0.574 40 :1@C2_:2@N3 52195 0.994 4.91 0.594 41 :1@N4_:2@O2 52174 0.994 4.31 0.748 42 :1@N3_:2@O2 52170 0.994 4.36 0.597 43 :1@N3_:2@C5 52163 0.994 4.64 0.644 44 :1@C4_:2@O4 52159 0.994 4.3 0.66 45 :1@N3_:2@C4 52126 0.993 4.57 0.672 46 :1@C2_:2@C4 52093 0.992 5.03 0.606 47 :1@O2_:2@N1 52068 0.992 4.7 0.667 48 :1@N4_:2@C5 52055 0.992 4.69 0.599 49 :1@N4_:2@C6 52024 0.991 5.01 0.528 50 :1@O2_:2@C6 52010 0.991 4.96 0.665 51 :1@C2_:2@O2 51989 0.99 5 0.572 52 :1@N4_:2@O4 51962 0.99 4.23 0.767 53 :1@C5_:2@O2 51938 0.989 5.12 0.72 54 :1@N1_:2@O4 51898 0.989 5.52 0.523 55 :1@N1_:2@O2 51715 0.985 5.63 0.488 56 :1@O2_:2@C2 51602 0.983 5.09 0.698 57 :1@C6_:2@O2 51150 0.974 5.66 0.598 58 :1@N3_:2@O4 50988 0.971 5.17 0.713 59 :1@O2_:2@O2 50728 0.966 5.33 0.713 60 :1@O2_:2@C5 50727 0.966 5.53 0.645 61 :1@C2_:2@O4 49695 0.947 5.71 0.593 62 :1@O2_:2@N3 49569 0.944 5.61 0.675 63 :1@O2_:2@C4 47670 0.908 5.84 0.617 64 :1@O2_:2@O4 31463 0.599 6.33 0.486 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 52498, 'v_base2' size 52498, output size 52498 TIME: Analyses took 0.0077 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 52498 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 52498 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 52498 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 52498 COM "COM" (double, distance), size is 52498 v_base1 "v_base1" (vector, vector), size is 52498 v_base2 "v_base2" (vector, vector), size is 52498 normalangle "normalangle" (double), size is 52498 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.7615 s ( 98.95%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0077 s ( 1.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7696 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: 0.9898 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.