CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 18:07:53 | Available memory: 52638.6 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.c0] Reading '../ctraj.c0' 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, 227214 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 227214 of 227214) Coordinate processing will occur on 227214 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.c0 (1-227214, 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 48 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@O4' 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@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' 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@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' 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@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' 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@O4' 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 227214 frames and processed 227214 frames. TIME: Trajectory processing: 1.0825 s TIME: Avg. throughput= 209899.7864 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 44.2703 48 # Contact Nframes Frac. Avg Stdev 1 :1@C2_:2@C5 224972 0.99 4.18 0.661 2 :1@N1_:2@C5 224793 0.989 4.44 0.602 3 :1@O2_:2@C5 224649 0.989 4.18 0.743 4 :1@N1_:2@C6 224335 0.987 4.85 0.564 5 :1@C2_:2@C6 223951 0.986 4.77 0.659 6 :1@O2_:2@C6 223743 0.985 4.62 0.745 7 :1@O2_:2@C4 223375 0.983 4.03 0.702 8 :1@C2_:2@C4 223339 0.983 4.13 0.657 9 :1@C2_:2@O4 222690 0.98 4.15 0.712 10 :1@N1_:2@C4 222602 0.98 4.69 0.675 11 :1@O2_:2@O4 222593 0.98 4.19 0.741 12 :1@N3_:2@C5 221340 0.974 4.46 0.79 13 :1@N1_:2@N1 221175 0.973 5.46 0.517 14 :1@N3_:2@C4 220847 0.972 4.2 0.824 15 :1@N3_:2@O4 220719 0.971 3.86 0.867 16 :1@O2_:2@N1 220314 0.97 4.9 0.755 17 :1@N1_:2@O4 220035 0.968 4.85 0.751 18 :1@O2_:2@N3 220017 0.968 4.26 0.88 19 :1@C2_:2@N1 219716 0.967 5.26 0.631 20 :1@C2_:2@N3 218769 0.963 4.61 0.82 21 :1@C6_:2@C5 218304 0.961 4.86 0.749 22 :1@O2_:2@C2 217163 0.956 4.7 0.885 23 :1@C6_:2@C6 215465 0.948 5.4 0.654 24 :1@N3_:2@C6 213867 0.941 5.27 0.694 25 :1@C4_:2@O4 213773 0.941 4.25 0.968 26 :1@C2_:2@C2 213488 0.94 5.15 0.753 27 :1@C4_:2@C5 212876 0.937 4.9 0.797 28 :1@N1_:2@N3 212288 0.934 5.18 0.76 29 :1@C4_:2@C4 211260 0.93 4.71 0.85 30 :1@N3_:2@N3 210505 0.926 4.78 0.852 31 :1@C5_:2@C5 210461 0.926 5.05 0.802 32 :1@C6_:2@C4 210027 0.924 5.12 0.788 33 :1@N1_:2@C2 205913 0.906 5.54 0.643 34 :1@C6_:2@O4 205719 0.905 5.09 0.86 35 :1@O4_:2@O4 205575 0.905 4.41 0.977 36 :1@C5_:2@O4 202238 0.89 4.8 0.917 37 :1@C5_:2@C4 201016 0.885 5.08 0.797 38 :1@N3_:2@N1 197504 0.869 5.77 0.624 39 :1@O4_:2@C4 196884 0.867 5.06 0.804 40 :1@O2_:2@O2 195883 0.862 5.13 0.938 41 :1@C5_:2@C6 193639 0.852 5.76 0.636 42 :1@N3_:2@C2 193212 0.85 5.5 0.703 43 :1@C4_:2@N3 189142 0.832 5.36 0.721 44 :1@C6_:2@N1 188056 0.828 6.05 0.511 45 :1@C6_:2@N3 184770 0.813 5.65 0.744 46 :1@C5_:2@N3 175153 0.771 5.73 0.704 47 :1@C6_:2@C2 164145 0.722 6.06 0.603 48 :1@N1_:2@O2 156522 0.689 6 0.678 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0143 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 227214 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 227214 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 227214 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 227214 COM "COM" (double, distance), size is 227214 v_base1 "v_base1" (vector), size is 227214 v_base2 "v_base2" (vector), size is 227214 normalangle "normalangle" (double), size is 227214 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: 1.5331 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.