CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 10:57:49 | Available memory: 86327.3 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] 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*), with fitting. [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_00001 Saving minimum observed distances in set 'Contacts_00001[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_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [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] [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,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3297 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 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. TIME: Run Initialization took 0.0002 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 61 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,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_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- traj.1.01 (1-50000, 1) ----- 0% 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 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@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@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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 29.5092 s TIME: Avg. throughput= 1694.3876 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 34.9885 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 33515 0.67 4.79 0.87 2 :1@N1_:2@C5 33126 0.663 4.73 0.814 3 :1@C6_:2@C5 31897 0.638 4.51 0.983 4 :1@C6_:2@C6 31763 0.635 4.74 1 5 :1@C2_:2@C5 31454 0.629 4.85 0.903 6 :1@C2_:2@C6 31276 0.626 4.88 0.878 7 :1@N1_:2@C4 30998 0.62 5.1 0.747 8 :1@N1_:2@N1 30892 0.618 5.14 0.781 9 :1@O2_:2@C6 30726 0.615 5.16 0.899 10 :1@C2_:2@C4 30007 0.6 5.05 0.88 11 :1@O2_:2@C5 29824 0.596 5.18 1.02 12 :1@C6_:2@C4 29704 0.594 4.74 0.851 13 :1@C5_:2@C5 29556 0.591 4.42 1.03 14 :1@N3_:2@C5 29533 0.591 4.84 0.92 15 :1@C2_:2@N1 29476 0.59 5.06 0.891 16 :1@N1_:2@N4 29455 0.589 5.45 0.799 17 :1@C6_:2@N4 28999 0.58 4.98 0.834 18 :1@N3_:2@C4 28962 0.579 4.8 0.947 19 :1@C4_:2@C5 28932 0.579 4.66 0.935 20 :1@O2_:2@N1 28911 0.578 5.24 0.877 21 :1@N1_:2@N3 28690 0.574 5.41 0.701 22 :1@C6_:2@N1 28640 0.573 5.09 0.888 23 :1@N3_:2@C6 28607 0.572 5 0.888 24 :1@C4_:2@N4 28451 0.569 4.6 0.98 25 :1@C2_:2@N3 28427 0.569 5.25 0.816 26 :1@C5_:2@C4 28366 0.567 4.39 0.956 27 :1@C5_:2@N4 28324 0.566 4.49 0.935 28 :1@C4_:2@C4 28322 0.566 4.49 0.936 29 :1@C5_:2@C6 28316 0.566 4.76 0.998 30 :1@N1_:2@C2 28295 0.566 5.4 0.666 31 :1@C2_:2@C2 27946 0.559 5.22 0.812 32 :1@N3_:2@N4 27939 0.559 4.96 1.04 33 :1@C2_:2@N4 27634 0.553 5.29 0.966 34 :1@C6_:2@N3 27623 0.552 5.12 0.803 35 :1@N3_:2@N3 27485 0.55 4.89 0.911 36 :1@C4_:2@C6 27358 0.547 4.93 0.91 37 :1@N4_:2@N4 27091 0.542 4.56 1.04 38 :1@O2_:2@C2 27083 0.542 5.44 0.866 39 :1@C6_:2@C2 26870 0.537 5.26 0.808 40 :1@O2_:2@C4 26729 0.535 5.31 0.992 41 :1@C5_:2@N3 26720 0.534 4.68 0.94 42 :1@C4_:2@N3 26693 0.534 4.6 0.925 43 :1@N3_:2@N1 26508 0.53 4.99 0.977 44 :1@N4_:2@C4 26487 0.53 4.6 0.949 45 :1@N4_:2@C5 26282 0.526 5.01 0.858 46 :1@N3_:2@C2 26124 0.522 4.92 0.95 47 :1@C5_:2@N1 25904 0.518 4.99 0.999 48 :1@O2_:2@N3 25804 0.516 5.49 0.911 49 :1@C5_:2@C2 25471 0.509 4.95 0.995 50 :1@C4_:2@C2 25243 0.505 4.79 1 51 :1@N4_:2@N3 25189 0.504 4.56 1.02 52 :1@C4_:2@N1 25038 0.501 4.94 0.978 53 :1@C2_:2@O2 24087 0.482 5.55 0.751 54 :1@N1_:2@O2 23911 0.478 5.89 0.61 55 :1@N4_:2@C6 23864 0.477 5.34 0.791 56 :1@N3_:2@O2 23072 0.461 5.14 0.913 57 :1@N4_:2@C2 22883 0.458 4.79 1.04 58 :1@O2_:2@O2 22772 0.455 5.66 0.843 59 :1@C6_:2@O2 22333 0.447 5.75 0.745 60 :1@C4_:2@O2 22208 0.444 5.05 0.967 61 :1@N4_:2@N1 21863 0.437 5.17 0.912 62 :1@C5_:2@O2 21748 0.435 5.34 0.933 63 :1@O2_:2@N4 21652 0.433 5.35 1.07 64 :1@N4_:2@O2 20365 0.407 4.85 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0024 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base2 "v_base2" (vector), size is 50000 v_base1 "v_base1" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- 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' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 30.0423 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.