CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 10:58:28 | Available memory: 87393.8 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 63 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@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: 36.2007 s TIME: Avg. throughput= 1381.1886 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 30.8882 63 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 31454 0.629 4.92 0.913 2 :1@N1_:2@C5 31182 0.624 4.81 0.866 3 :1@C6_:2@C5 29752 0.595 4.63 1.03 4 :1@C6_:2@C6 29273 0.585 4.88 1.03 5 :1@C2_:2@C5 29004 0.58 4.92 0.937 6 :1@N1_:2@C4 28732 0.575 5.09 0.786 7 :1@C2_:2@C6 28538 0.571 5.01 0.918 8 :1@N1_:2@N1 28349 0.567 5.23 0.808 9 :1@O2_:2@C6 27893 0.558 5.23 0.911 10 :1@C6_:2@C4 27526 0.551 4.78 0.897 11 :1@O2_:2@C5 27507 0.55 5.2 1.03 12 :1@C2_:2@C4 27335 0.547 5.06 0.904 13 :1@N1_:2@N4 27322 0.546 5.37 0.835 14 :1@C6_:2@N4 26825 0.536 4.96 0.873 15 :1@C5_:2@C5 26771 0.535 4.57 1.07 16 :1@N3_:2@C5 26430 0.529 4.94 0.945 17 :1@N1_:2@N3 26317 0.526 5.38 0.738 18 :1@C2_:2@N1 26185 0.524 5.16 0.909 19 :1@C6_:2@N1 25991 0.52 5.19 0.916 20 :1@N3_:2@C4 25888 0.518 4.86 0.963 21 :1@C5_:2@N4 25823 0.516 4.54 0.98 22 :1@N1_:2@C2 25800 0.516 5.43 0.696 23 :1@C5_:2@C4 25723 0.514 4.48 1.01 24 :1@O2_:2@N1 25624 0.512 5.32 0.888 25 :1@C4_:2@C5 25619 0.512 4.78 0.959 26 :1@C2_:2@N3 25588 0.512 5.26 0.842 27 :1@C4_:2@N4 25558 0.511 4.64 0.999 28 :1@C2_:2@N4 25464 0.509 5.25 0.996 29 :1@C4_:2@C4 25330 0.507 4.59 0.977 30 :1@C6_:2@N3 25235 0.505 5.11 0.831 31 :1@N3_:2@N4 25202 0.504 4.95 1.06 32 :1@C5_:2@C6 24990 0.5 4.89 1.02 33 :1@N3_:2@C6 24902 0.498 5.1 0.903 34 :1@C2_:2@C2 24885 0.498 5.28 0.835 35 :1@O2_:2@C4 24506 0.49 5.29 1.01 36 :1@C6_:2@C2 24382 0.488 5.29 0.831 37 :1@N3_:2@N3 24264 0.485 4.94 0.934 38 :1@N4_:2@N4 24009 0.48 4.64 1.06 39 :1@C5_:2@N3 24007 0.48 4.74 0.98 40 :1@O2_:2@C2 23884 0.478 5.47 0.877 41 :1@C4_:2@N3 23685 0.474 4.69 0.98 42 :1@C4_:2@C6 23597 0.472 5.04 0.923 43 :1@O2_:2@N3 23229 0.465 5.47 0.933 44 :1@N4_:2@C4 23154 0.463 4.71 0.977 45 :1@N3_:2@N1 22704 0.454 5.09 0.99 46 :1@N3_:2@C2 22680 0.454 5.01 0.977 47 :1@N4_:2@C5 22657 0.453 5.12 0.866 48 :1@C5_:2@N1 22559 0.451 5.08 1.02 49 :1@C5_:2@C2 22422 0.448 5.01 1.02 50 :1@C4_:2@C2 21831 0.437 4.88 1.04 51 :1@N4_:2@N3 21760 0.435 4.66 1.06 52 :1@N1_:2@O2 21372 0.427 5.87 0.632 53 :1@C4_:2@N1 21339 0.427 5.04 1 54 :1@C2_:2@O2 21087 0.422 5.59 0.783 55 :1@C6_:2@O2 20135 0.403 5.75 0.76 56 :1@N4_:2@C6 19930 0.399 5.43 0.79 57 :1@O2_:2@O2 19683 0.394 5.67 0.862 58 :1@N3_:2@O2 19672 0.393 5.2 0.944 59 :1@N4_:2@C2 19192 0.384 4.86 1.07 60 :1@C5_:2@O2 18919 0.378 5.36 0.953 61 :1@C4_:2@O2 18881 0.378 5.09 0.993 62 :1@N4_:2@N1 17946 0.359 5.23 0.911 63 :1@N4_:2@O2 16907 0.338 4.89 1.09 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: 36.9186 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.