CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 14:47:48 | Available memory: 2.672 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,N4,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,N4,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,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,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, 61 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 40686 of 40686) Coordinate processing will occur on 40686 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,N4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-40686, 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,N4,N3,C2,O2] corresponds to 8 atoms. Setup 62 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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@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@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 40686 frames and processed 40686 frames. TIME: Avg. throughput= 139648.3906 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 61.5223 62 # Contact Nframes Frac. Avg Stdev 1 :1@C5_:2@C5 40686 1 3.65 0.344 2 :1@C5_:2@C4 40686 1 3.7 0.347 3 :1@C6_:2@C5 40686 1 3.77 0.329 4 :1@C6_:2@C6 40686 1 3.9 0.34 5 :1@C4_:2@N3 40686 1 3.93 0.409 6 :1@C4_:2@C2 40686 1 3.98 0.42 7 :1@C5_:2@C6 40686 1 3.98 0.396 8 :1@N4_:2@C2 40686 1 4.02 0.516 9 :1@C5_:2@N4 40686 1 4.05 0.494 10 :1@C5_:2@N3 40686 1 4.07 0.483 11 :1@N1_:2@C6 40686 1 4.08 0.329 12 :1@C4_:2@N1 40686 1 4.14 0.436 13 :1@N3_:2@N1 40686 1 4.15 0.478 14 :1@C4_:2@C6 40686 1 4.24 0.433 15 :1@C6_:2@C4 40686 1 4.27 0.404 16 :1@C2_:2@N1 40686 1 4.31 0.458 17 :1@C5_:2@N1 40686 1 4.31 0.555 18 :1@C5_:2@C2 40686 1 4.34 0.607 19 :1@N1_:2@C5 40686 1 4.36 0.431 20 :1@N1_:2@N1 40686 1 4.47 0.306 21 :1@C6_:2@N1 40686 1 4.47 0.47 22 :1@N4_:2@N1 40686 1 4.58 0.54 23 :1@N1_:2@C2 40686 1 5.08 0.384 24 :1@N4_:2@N3 40685 1 3.8 0.467 25 :1@C4_:2@C4 40685 1 3.99 0.526 26 :1@C4_:2@C5 40685 1 4.16 0.542 27 :1@N3_:2@C2 40685 1 4.21 0.502 28 :1@C2_:2@C6 40685 1 4.34 0.539 29 :1@C6_:2@N3 40685 1 4.8 0.495 30 :1@N3_:2@C6 40684 1 4.42 0.565 31 :1@C6_:2@C2 40683 1 4.88 0.535 32 :1@N1_:2@C4 40683 1 4.99 0.45 33 :1@C6_:2@N4 40682 1 4.75 0.498 34 :1@C4_:2@O2 40680 1 4.45 0.598 35 :1@N4_:2@C4 40676 1 4.1 0.619 36 :1@N4_:2@O2 40676 1 4.26 0.72 37 :1@C2_:2@C2 40674 1 4.76 0.503 38 :1@N4_:2@C6 40671 1 4.88 0.508 39 :1@N1_:2@N3 40666 1 5.33 0.432 40 :1@N3_:2@N3 40664 0.999 4.52 0.626 41 :1@C2_:2@C5 40661 0.999 4.8 0.63 42 :1@N3_:2@O2 40652 0.999 4.53 0.536 43 :1@N4_:2@C5 40632 0.999 4.66 0.613 44 :1@N3_:2@C5 40623 0.998 4.7 0.686 45 :1@C4_:2@N4 40612 0.998 4.49 0.715 46 :1@N3_:2@C4 40600 0.998 4.72 0.713 47 :1@O2_:2@N1 40592 0.998 4.83 0.668 48 :1@C2_:2@N3 40584 0.997 5.19 0.585 49 :1@C2_:2@O2 40549 0.997 5.22 0.522 50 :1@C2_:2@C4 40539 0.996 5.18 0.633 51 :1@C5_:2@O2 40518 0.996 5.09 0.758 52 :1@O2_:2@C6 40511 0.996 5.01 0.687 53 :1@N4_:2@N4 40476 0.995 4.42 0.833 54 :1@N1_:2@O2 40291 0.99 5.79 0.449 55 :1@N1_:2@N4 40173 0.987 5.68 0.521 56 :1@O2_:2@C2 40063 0.985 5.36 0.686 57 :1@C6_:2@O2 39699 0.976 5.7 0.608 58 :1@O2_:2@O2 39079 0.961 5.63 0.665 59 :1@N3_:2@N4 39022 0.959 5.38 0.754 60 :1@O2_:2@C5 38970 0.958 5.63 0.674 61 :1@O2_:2@N3 36243 0.891 5.88 0.641 62 :1@O2_:2@C4 34680 0.852 5.94 0.612 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 40686, 'v_base2' size 40686, output size 40686 TIME: Analyses took 0.0029 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 40686 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 40686 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 40686 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 40686 COM "COM" (double, distance), size is 40686 v_base1 "v_base1" (vector, vector), size is 40686 v_base2 "v_base2" (vector, vector), size is 40686 normalangle "normalangle" (double), size is 40686 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2913 s ( 98.95%) TIME: Action Post : 0.0001 s ( 0.04%) TIME: Analysis : 0.0029 s ( 0.99%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2944 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: 0.4031 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.