CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/16 04:58:42 | Available memory: 1.309 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] Reading '../../traj.1.01' as Amber NetCDF [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3296 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped topology: 60 atoms, 2 res, box: Orthogonal, 1 mol 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. ----- traj.1.01 (1-50000, 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 50000 frames and processed 50000 frames. TIME: Avg. throughput= 73.5769 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 31.6485 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 31109 0.622 4.91 0.922 2 :1@N1_:2@C5 30729 0.615 4.82 0.868 3 :1@C6_:2@C5 29134 0.583 4.62 1.03 4 :1@C2_:2@C5 28901 0.578 4.93 0.911 5 :1@C6_:2@C6 28837 0.577 4.87 1.01 6 :1@C2_:2@C6 28588 0.572 4.98 0.919 7 :1@N1_:2@C4 28444 0.569 5.07 0.769 8 :1@N1_:2@N1 28363 0.567 5.16 0.832 9 :1@O2_:2@C6 28289 0.566 5.2 0.906 10 :1@O2_:2@C5 27839 0.557 5.24 1 11 :1@C2_:2@C4 27356 0.547 5.03 0.875 12 :1@C6_:2@C4 27279 0.546 4.74 0.905 13 :1@N1_:2@O4 27130 0.543 5.39 0.797 14 :1@C6_:2@O4 26566 0.531 4.93 0.896 15 :1@N1_:2@N3 26484 0.53 5.27 0.749 16 :1@C2_:2@N1 26455 0.529 5.04 0.934 17 :1@N3_:2@C5 26417 0.528 4.92 0.919 18 :1@C5_:2@C5 26370 0.527 4.54 1.05 19 :1@O2_:2@N1 26339 0.527 5.2 0.913 20 :1@N3_:2@C4 26072 0.521 4.8 0.953 21 :1@C6_:2@N1 26070 0.521 5.16 0.9 22 :1@C2_:2@O4 25844 0.517 5.3 0.931 23 :1@N1_:2@C2 25830 0.517 5.31 0.73 24 :1@C2_:2@N3 25819 0.516 5.1 0.871 25 :1@C5_:2@C4 25709 0.514 4.41 1.02 26 :1@C5_:2@O4 25582 0.512 4.47 0.989 27 :1@C4_:2@C5 25552 0.511 4.75 0.942 28 :1@C6_:2@N3 25550 0.511 5.03 0.841 29 :1@N3_:2@O4 25500 0.51 4.97 0.995 30 :1@C4_:2@O4 25489 0.51 4.59 0.965 31 :1@C4_:2@C4 25344 0.507 4.5 0.97 32 :1@O2_:2@C4 25287 0.506 5.34 1 33 :1@N3_:2@C6 25262 0.505 5.06 0.9 34 :1@C2_:2@C2 25177 0.504 5.09 0.894 35 :1@C5_:2@C6 24981 0.5 4.88 0.985 36 :1@O2_:2@C2 24722 0.494 5.3 0.926 37 :1@C6_:2@C2 24646 0.493 5.24 0.833 38 :1@N3_:2@N3 24559 0.491 4.75 0.988 39 :1@O2_:2@N3 24411 0.488 5.38 0.96 40 :1@C5_:2@N3 24333 0.487 4.64 1.01 41 :1@C4_:2@N3 24072 0.481 4.53 1.05 42 :1@N4_:2@O4 24001 0.48 4.57 1.02 43 :1@C4_:2@C6 23838 0.477 5.01 0.897 44 :1@N4_:2@C4 23445 0.469 4.61 0.979 45 :1@N3_:2@N1 23364 0.467 4.97 0.999 46 :1@N3_:2@C2 23180 0.464 4.8 1.03 47 :1@N4_:2@C5 22848 0.457 5.09 0.85 48 :1@C5_:2@C2 22831 0.457 4.95 1.02 49 :1@C5_:2@N1 22817 0.456 5.05 0.974 50 :1@C4_:2@C2 22142 0.443 4.72 1.06 51 :1@N4_:2@N3 22096 0.442 4.48 1.1 52 :1@N1_:2@O2 22081 0.442 5.71 0.704 53 :1@C4_:2@N1 21877 0.438 4.96 0.971 54 :1@C2_:2@O2 21823 0.436 5.33 0.857 55 :1@O2_:2@O2 21153 0.423 5.44 0.935 56 :1@O2_:2@O4 20919 0.418 5.44 1.08 57 :1@C6_:2@O2 20753 0.415 5.66 0.79 58 :1@N4_:2@C6 20571 0.411 5.42 0.771 59 :1@N3_:2@O2 20551 0.411 4.92 0.989 60 :1@N4_:2@C2 19725 0.395 4.7 1.04 61 :1@C4_:2@O2 19659 0.393 4.89 0.992 62 :1@C5_:2@O2 19560 0.391 5.27 0.94 63 :1@N4_:2@N1 18812 0.376 5.18 0.858 64 :1@N4_:2@O2 17938 0.359 4.73 1.04 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 50000, 'v_base2' size 50000, output size 50000 TIME: Analyses took 0.0060 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 50000 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector, vector), size is 50000 v_base2 "v_base2" (vector, vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 679.5611 s ( 99.98%) TIME: Action Post : 0.1594 s ( 0.02%) TIME: Analysis : 0.0060 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0003 s ( 0.00%) TIME: Run Total 679.7270 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 683.9951 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.