CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/10/15 11:39:04 | Available memory: 88710.7 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,C2,N3,C4,C5,C6 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9', 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,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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', 4374 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 0.0360 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 4311 atoms. Stripped parm: 'full.topo.hmr', 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*](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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6] corresponds to 6 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6 potential contact sites for ':1@N1,C2,N3,C4,C5,C6' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 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,C2,N3,C4,C5,C6] corresponds to 6 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 52 native contacts: Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C6' to ':2@N9' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 73.7431 s TIME: Avg. throughput= 678.0300 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 31.6632 52 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@N7 34714 0.694 5.01 0.88 2 :1@N1_:2@C5 34537 0.691 4.85 0.785 3 :1@N1_:2@C8 34040 0.681 5.31 0.894 4 :1@N1_:2@C4 33742 0.675 5.11 0.714 5 :1@N1_:2@C6 33471 0.669 4.83 0.863 6 :1@N1_:2@N9 33298 0.666 5.43 0.772 7 :1@C6_:2@C5 33255 0.665 4.84 0.849 8 :1@C6_:2@N7 33097 0.662 5.01 0.993 9 :1@C6_:2@C6 32945 0.659 4.72 0.887 10 :1@C2_:2@C5 32804 0.656 5.01 0.861 11 :1@C6_:2@N6 32260 0.645 4.75 0.966 12 :1@N1_:2@N3 32257 0.645 5.33 0.765 13 :1@C2_:2@C6 32255 0.645 4.88 0.904 14 :1@N1_:2@N6 32247 0.645 4.97 0.946 15 :1@C6_:2@C4 32166 0.643 5.2 0.795 16 :1@N1_:2@N1 32150 0.643 5.03 0.929 17 :1@C2_:2@N7 31693 0.634 5.19 0.96 18 :1@C6_:2@N1 31692 0.634 4.94 0.954 19 :1@N1_:2@C2 31629 0.633 5.22 0.889 20 :1@C2_:2@C4 31608 0.632 5.25 0.829 21 :1@C5_:2@C6 31293 0.626 4.68 0.925 22 :1@C5_:2@N6 31260 0.625 4.55 0.992 23 :1@C6_:2@C8 31241 0.625 5.39 0.977 24 :1@C2_:2@N1 31090 0.622 4.99 0.942 25 :1@C2_:2@N6 30983 0.62 4.92 1.04 26 :1@N3_:2@C6 30801 0.616 4.86 0.93 27 :1@C4_:2@N6 30624 0.612 4.61 0.985 28 :1@C4_:2@C6 30586 0.612 4.77 0.949 29 :1@C5_:2@N1 30584 0.612 4.85 0.956 30 :1@C6_:2@N3 30572 0.611 5.42 0.835 31 :1@C5_:2@C5 30528 0.611 4.97 0.969 32 :1@C6_:2@C2 30507 0.61 5.22 0.911 33 :1@C2_:2@C2 30443 0.609 5.21 0.936 34 :1@N3_:2@N6 30296 0.606 4.77 1.04 35 :1@C6_:2@N9 30294 0.606 5.56 0.85 36 :1@N3_:2@N1 30139 0.603 4.93 0.962 37 :1@C2_:2@N3 30055 0.601 5.36 0.865 38 :1@C4_:2@N1 29976 0.6 4.86 0.964 39 :1@N3_:2@C5 29744 0.595 5.13 0.944 40 :1@C2_:2@N9 28883 0.578 5.55 0.902 41 :1@C4_:2@C5 28863 0.577 5.1 1 42 :1@C5_:2@N7 28844 0.577 5.16 1.07 43 :1@C5_:2@C2 28381 0.568 5.21 0.968 44 :1@C5_:2@C4 28007 0.56 5.35 0.962 45 :1@N3_:2@C2 27941 0.559 5.17 0.995 46 :1@C4_:2@C2 27124 0.542 5.17 1.02 47 :1@N3_:2@C4 26793 0.536 5.35 0.977 48 :1@C5_:2@N3 25966 0.519 5.45 0.964 49 :1@N3_:2@N3 25067 0.501 5.34 0.991 50 :1@C4_:2@C4 24994 0.5 5.35 1.02 51 :1@C4_:2@N3 23282 0.466 5.35 1.03 52 :1@C5_:2@N9 22138 0.443 5.6 0.949 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0731 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: 76.9674 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.