CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/16 05:18:50 | Available memory: 1.388 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,N4,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,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,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,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,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,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. [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,O4,N3,C2,O2 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,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,O4,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,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 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,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,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. ----- 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,N4,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@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@O4' to ':2@N1' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@N4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' Atom ':1@O4' 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@N4' 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@N4' 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= 98.0883 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 28.9154 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 29801 0.596 5.06 0.889 2 :1@N1_:2@C5 29559 0.591 4.85 0.883 3 :1@C6_:2@C5 28178 0.564 4.82 1.01 4 :1@C6_:2@C6 27703 0.554 5.13 0.989 5 :1@C2_:2@C5 27193 0.544 4.87 0.988 6 :1@N1_:2@C4 27158 0.543 5.03 0.839 7 :1@C2_:2@C6 26636 0.533 5.08 0.935 8 :1@N1_:2@N1 26538 0.531 5.34 0.786 9 :1@C6_:2@C4 25866 0.517 4.88 0.918 10 :1@N1_:2@N4 25842 0.517 5.23 0.85 11 :1@O2_:2@C6 25737 0.515 5.14 0.991 12 :1@O2_:2@C5 25666 0.513 5 1.08 13 :1@C2_:2@C4 25546 0.511 4.88 0.977 14 :1@C6_:2@N4 25248 0.505 4.98 0.913 15 :1@C5_:2@C5 24914 0.498 4.82 1.04 16 :1@N1_:2@N3 24640 0.493 5.28 0.793 17 :1@N3_:2@C5 24536 0.491 4.92 0.973 18 :1@C2_:2@N1 24327 0.487 5.24 0.912 19 :1@C2_:2@N4 24314 0.486 4.99 1.01 20 :1@C5_:2@N4 24165 0.483 4.64 1.02 21 :1@N3_:2@C4 24142 0.483 4.74 1.04 22 :1@C6_:2@N1 24111 0.482 5.4 0.888 23 :1@N1_:2@C2 24048 0.481 5.41 0.734 24 :1@C5_:2@C4 23921 0.478 4.68 1 25 :1@N3_:2@N4 23862 0.477 4.71 1.1 26 :1@C2_:2@N3 23824 0.476 5.06 0.946 27 :1@O2_:2@N1 23710 0.474 5.23 0.987 28 :1@C4_:2@N4 23674 0.473 4.57 1.04 29 :1@C6_:2@N3 23488 0.47 5.18 0.872 30 :1@O2_:2@C4 23470 0.469 4.98 1.05 31 :1@C4_:2@C5 23466 0.469 4.95 0.942 32 :1@C4_:2@C4 23241 0.465 4.67 0.986 33 :1@C2_:2@C2 23091 0.462 5.21 0.908 34 :1@N3_:2@C6 22923 0.458 5.24 0.891 35 :1@C5_:2@C6 22904 0.458 5.2 0.966 36 :1@N3_:2@N3 22515 0.45 4.84 1.03 37 :1@C6_:2@C2 22493 0.45 5.41 0.852 38 :1@O2_:2@C2 22348 0.447 5.22 1.01 39 :1@O2_:2@N3 22204 0.444 5.12 1.02 40 :1@O4_:2@N4 22115 0.442 4.63 1.07 41 :1@C5_:2@N3 22063 0.441 4.93 0.995 42 :1@C4_:2@N3 21575 0.431 4.8 1.01 43 :1@O2_:2@N4 21308 0.426 5.06 1.09 44 :1@C4_:2@C6 21122 0.422 5.34 0.854 45 :1@O4_:2@C4 21098 0.422 4.86 0.957 46 :1@N3_:2@C2 20830 0.417 5.08 0.995 47 :1@N3_:2@N1 20657 0.413 5.27 0.933 48 :1@O4_:2@C5 20339 0.407 5.3 0.838 49 :1@C5_:2@C2 20217 0.404 5.26 1.01 50 :1@C5_:2@N1 20203 0.404 5.39 0.979 51 :1@N1_:2@O2 19989 0.4 5.82 0.688 52 :1@C2_:2@O2 19670 0.393 5.51 0.858 53 :1@O4_:2@N3 19586 0.392 4.88 1.03 54 :1@C4_:2@C2 19520 0.39 5.13 1.01 55 :1@O2_:2@O2 18835 0.377 5.43 1 56 :1@C4_:2@N1 18805 0.376 5.39 0.92 57 :1@N3_:2@O2 18069 0.361 5.3 0.98 58 :1@C6_:2@O2 17675 0.353 5.76 0.8 59 :1@O4_:2@C6 17198 0.344 5.73 0.746 60 :1@O4_:2@C2 16708 0.334 5.22 1.02 61 :1@C4_:2@O2 16381 0.328 5.32 1.02 62 :1@C5_:2@O2 15916 0.318 5.48 0.972 63 :1@O4_:2@N1 15015 0.3 5.61 0.852 64 :1@O4_:2@O2 13873 0.277 5.2 1.07 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 0.0066 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 : 509.7448 s ( 99.97%) TIME: Action Post : 0.1594 s ( 0.03%) TIME: Analysis : 0.0066 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0012 s ( 0.00%) TIME: Run Total 509.9122 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: 511.0006 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.