CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 03/28/16 14:00:50 | Available memory: 1.570 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,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_base2 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] [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] [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, 3319 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 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 3256 atoms. Stripped topology: 63 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,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 (10 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (10 atoms), imaged. 5: [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. 6: [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. ----- traj.1.01 (1-50000, 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 57 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@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@O4' to ':2@C5' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' 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= 97.4717 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 30.8184 57 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 32378 0.648 4.72 0.916 2 :1@N1_:2@C5 32267 0.645 4.7 0.821 3 :1@C6_:2@C5 31353 0.627 4.71 0.899 4 :1@C6_:2@C6 30798 0.616 4.83 0.969 5 :1@N1_:2@C4 30649 0.613 4.94 0.781 6 :1@N1_:2@N1 30449 0.609 4.91 0.893 7 :1@C2_:2@C5 30393 0.608 4.79 0.869 8 :1@C2_:2@C6 30075 0.602 4.86 0.917 9 :1@C6_:2@C4 30064 0.601 4.79 0.846 10 :1@O2_:2@C6 29934 0.599 5.09 0.855 11 :1@O2_:2@C5 29774 0.595 5.08 0.876 12 :1@N1_:2@O4 29265 0.585 5.32 0.788 13 :1@C2_:2@C4 29155 0.583 4.9 0.867 14 :1@C6_:2@O4 29140 0.583 5.07 0.855 15 :1@N1_:2@N3 28954 0.579 5.06 0.769 16 :1@N1_:2@C2 28641 0.573 5.07 0.791 17 :1@C6_:2@N1 28621 0.572 4.97 0.99 18 :1@C6_:2@N3 28372 0.567 4.91 0.825 19 :1@C5_:2@C5 28326 0.567 4.77 0.925 20 :1@O2_:2@C4 28111 0.562 5.27 0.9 21 :1@C5_:2@C4 28097 0.562 4.6 0.941 22 :1@N3_:2@C5 28047 0.561 4.88 0.941 23 :1@C2_:2@O4 28042 0.561 5.2 0.891 24 :1@C5_:2@O4 27913 0.558 4.71 0.919 25 :1@C2_:2@N1 27847 0.557 4.94 0.986 26 :1@O2_:2@N1 27760 0.555 5.15 1.02 27 :1@C6_:2@C2 27547 0.551 5.01 0.89 28 :1@N3_:2@C4 27485 0.55 4.7 0.993 29 :1@C2_:2@N3 27473 0.549 4.95 0.899 30 :1@N3_:2@O4 27189 0.544 4.85 0.992 31 :1@C4_:2@O4 27041 0.541 4.62 0.982 32 :1@C4_:2@C4 26771 0.535 4.56 1.02 33 :1@C4_:2@C5 26585 0.532 4.87 0.929 34 :1@C2_:2@C2 26582 0.532 4.97 0.969 35 :1@C5_:2@C6 26468 0.529 4.99 0.924 36 :1@C5_:2@N3 26467 0.529 4.65 0.961 37 :1@O2_:2@N3 26324 0.526 5.31 0.945 38 :1@N3_:2@C6 26061 0.521 5.03 0.884 39 :1@N1_:2@O2 25944 0.519 5.51 0.753 40 :1@N3_:2@N3 25593 0.512 4.65 1.03 41 :1@O2_:2@C2 25388 0.508 5.19 1.04 42 :1@C4_:2@N3 25103 0.502 4.5 1.05 43 :1@O4_:2@O4 25076 0.502 4.63 1.04 44 :1@O2_:2@O4 24766 0.495 5.46 0.961 45 :1@C6_:2@O2 24652 0.493 5.4 0.86 46 :1@C5_:2@C2 24586 0.492 4.85 1.01 47 :1@C4_:2@C6 24177 0.484 5.11 0.848 48 :1@C5_:2@N1 24119 0.482 4.99 0.98 49 :1@O4_:2@C4 24085 0.482 4.69 0.988 50 :1@N3_:2@C2 23835 0.477 4.76 1.03 51 :1@N3_:2@N1 23651 0.473 4.94 0.917 52 :1@C2_:2@O2 23326 0.467 5.23 0.977 53 :1@O4_:2@C5 23078 0.462 5.21 0.82 54 :1@C4_:2@C2 22881 0.458 4.72 0.981 55 :1@O4_:2@N3 22466 0.449 4.53 1.02 56 :1@N3_:2@O2 21497 0.43 4.96 1.06 57 :1@O2_:2@O2 20277 0.406 5.18 1.06 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 0.0036 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_base2 "v_base2" (vector, vector), size is 50000 v_base1 "v_base1" (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 : 512.9695 s ( 99.94%) TIME: Action Post : 0.3012 s ( 0.06%) TIME: Analysis : 0.0036 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0005 s ( 0.00%) TIME: Run Total 513.2749 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 513.8077 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.