CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/07/16 23:28:47 | Available memory: 1.363 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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, 3298 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: 62 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*](39) Reference mask: [:1,2&!@H*](39) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 39 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@N6' to ':2@O2' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' 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@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@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' 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= 63.7055 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 22.3281 39 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C6 34106 0.682 4.77 0.988 2 :1@N3_:2@C5 33315 0.666 4.8 0.963 3 :1@C4_:2@C6 33082 0.662 4.74 0.969 4 :1@N3_:2@N1 32495 0.65 4.85 0.967 5 :1@N9_:2@N1 31718 0.634 5.27 0.778 6 :1@N3_:2@C4 31540 0.631 4.98 0.895 7 :1@C4_:2@C4 31427 0.629 4.75 0.827 8 :1@C4_:2@N1 31294 0.626 4.95 0.914 9 :1@C2_:2@C6 31146 0.623 4.95 0.971 10 :1@N3_:2@C2 30658 0.613 4.99 0.904 11 :1@C2_:2@C5 30620 0.612 4.93 0.974 12 :1@N3_:2@N3 30528 0.611 5.06 0.865 13 :1@C4_:2@N3 30194 0.604 4.95 0.822 14 :1@C2_:2@N1 30168 0.603 4.81 1.04 15 :1@C4_:2@C2 29679 0.594 5.04 0.844 16 :1@C2_:2@C4 29623 0.592 4.89 0.955 17 :1@C2_:2@N3 29376 0.588 4.83 0.979 18 :1@C2_:2@C2 29197 0.584 4.76 1.06 19 :1@N3_:2@O4 29100 0.582 5.3 0.936 20 :1@N9_:2@C2 29017 0.58 5.47 0.731 21 :1@N1_:2@C4 28652 0.573 4.76 0.95 22 :1@N1_:2@N3 28118 0.562 4.6 1.02 23 :1@N1_:2@C6 28075 0.561 5.17 0.899 24 :1@C6_:2@N3 27621 0.552 4.47 1.01 25 :1@C5_:2@N1 27523 0.55 5 0.938 26 :1@C2_:2@O4 27408 0.548 5.11 1.02 27 :1@C5_:2@C2 27256 0.545 4.89 0.957 28 :1@N3_:2@O2 27193 0.544 5.28 0.869 29 :1@N1_:2@N1 27106 0.542 4.94 1 30 :1@N1_:2@C2 27016 0.54 4.63 1.08 31 :1@C4_:2@O2 26301 0.526 5.44 0.798 32 :1@C6_:2@C2 26119 0.522 4.68 1.02 33 :1@C2_:2@O2 26053 0.521 4.81 1.01 34 :1@C6_:2@N1 25760 0.515 5 0.932 35 :1@N1_:2@O2 24474 0.489 4.6 1.03 36 :1@C5_:2@O2 24428 0.489 5.24 0.923 37 :1@C6_:2@O2 23947 0.479 4.83 1.01 38 :1@N9_:2@O2 23370 0.467 5.9 0.725 39 :1@N6_:2@O2 21703 0.434 4.89 1.03 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 0.0062 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 : 0.0002 s ( 0.00%) TIME: Trajectory Process : 784.8614 s ( 99.98%) TIME: Action Post : 0.1885 s ( 0.02%) TIME: Analysis : 0.0062 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0011 s ( 0.00%) TIME: Run Total 785.0575 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: 788.3073 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.