CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 18:08:14 | Available memory: 52614.5 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c5] Reading '../ctraj.c5' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,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,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_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,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol, 39854 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 39854 of 39854) Coordinate processing will occur on 39854 frames. TIME: Run Initialization took 0.0005 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 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,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,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,O4,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,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Vector 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] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms. ----- ctraj.c5 (1-39854, 1) ----- 0% 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,O4,N3,C2,O2] corresponds to 8 atoms. Setup 28 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' 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@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@N3' Atom ':1@C4' to ':2@C2' Atom ':1@O4' to ':2@N1' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' Atom ':1@N3' to ':2@C6' Atom ':1@C2' to ':2@C6' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 39854 frames and processed 39854 frames. TIME: Trajectory processing: 0.1788 s TIME: Avg. throughput= 222867.1767 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 7.92759 28 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 21376 0.536 6.12 0.737 2 :1@C2_:2@C6 19745 0.495 5.99 0.853 3 :1@N1_:2@N1 18978 0.476 6.16 0.702 4 :1@C6_:2@C6 17976 0.451 6.21 0.592 5 :1@C6_:2@N1 17846 0.448 6.16 0.62 6 :1@C5_:2@N1 16610 0.417 6.09 0.659 7 :1@C4_:2@N1 15598 0.391 6.07 0.768 8 :1@N3_:2@C6 15435 0.387 6.06 0.77 9 :1@C5_:2@C6 14738 0.37 6.26 0.567 10 :1@C4_:2@C6 13105 0.329 6.23 0.653 11 :1@N1_:2@C5 12046 0.302 6.03 0.846 12 :1@O4_:2@N1 11639 0.292 6.13 0.76 13 :1@C4_:2@C2 10786 0.271 5.81 1.09 14 :1@C5_:2@C2 10661 0.268 5.99 0.912 15 :1@C5_:2@O2 9555 0.24 5.8 1.08 16 :1@C6_:2@C5 9400 0.236 6.27 0.619 17 :1@O4_:2@C2 9227 0.232 5.81 1.04 18 :1@C6_:2@C2 9003 0.226 5.98 0.866 19 :1@O4_:2@C6 7668 0.192 6.25 0.656 20 :1@C5_:2@C5 7529 0.189 6.34 0.584 21 :1@C6_:2@O2 7142 0.179 5.7 1.1 22 :1@C4_:2@C5 7129 0.179 6.16 0.725 23 :1@C4_:2@N3 6189 0.155 5.49 1.06 24 :1@C5_:2@N3 5788 0.145 5.86 0.863 25 :1@O4_:2@N3 5656 0.142 5.57 1.03 26 :1@C6_:2@N3 5412 0.136 5.87 0.756 27 :1@C4_:2@C4 5109 0.128 5.77 0.828 28 :1@C5_:2@C4 4600 0.115 6.12 0.669 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0018 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 39854 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 39854 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 39854 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 39854 COM "COM" (double, distance), size is 39854 v_base1 "v_base1" (vector), size is 39854 v_base2 "v_base2" (vector), size is 39854 normalangle "normalangle" (double), size is 39854 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.2790 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.