CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 16:15:45 | Available memory: 866.371 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.c6] Reading '../ctraj.c6' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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_00002 Saving minimum observed distances in set 'Contacts_00002[mindist]' Contact stats will be written to 'STDOUT' Contact res pairs will be written to 'STDOUT' [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES: 0: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27794 of 27794) Coordinate processing will occur on 27794 frames. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c6 (1-27794, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 31 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@O6' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 27794 frames and processed 27794 frames. TIME: Trajectory processing: 0.3228 s TIME: Avg. throughput= 86097.7823 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 9.82313 31 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 17072 0.614 6.11 0.588 2 :1@C4_:2@N9 16120 0.58 6.09 0.513 3 :1@N9_:2@N9 15279 0.55 6.06 0.606 4 :1@C2_:2@N9 14958 0.538 6.22 0.565 5 :1@N9_:2@C8 14144 0.509 5.98 0.881 6 :1@C4_:2@C8 13867 0.499 6.07 0.773 7 :1@N3_:2@C8 12894 0.464 6.08 0.892 8 :1@C8_:2@C8 11809 0.425 5.93 0.919 9 :1@C5_:2@C8 11764 0.423 6.14 0.65 10 :1@N2_:2@N9 11323 0.407 6.12 0.816 11 :1@N9_:2@C4 10978 0.395 5.86 0.748 12 :1@N3_:2@C4 10675 0.384 6.14 0.605 13 :1@N9_:2@N7 9452 0.34 5.89 1.09 14 :1@C8_:2@N7 9182 0.33 5.8 1.23 15 :1@N9_:2@C5 9157 0.329 5.97 0.772 16 :1@C2_:2@C8 9026 0.325 6.14 0.909 17 :1@C4_:2@C5 7941 0.286 6.27 0.525 18 :1@C4_:2@N7 7514 0.27 5.97 0.96 19 :1@N1_:2@C8 7313 0.263 6.31 0.675 20 :1@C5_:2@N7 7106 0.256 6.06 0.857 21 :1@N9_:2@C6 6502 0.234 6.02 0.659 22 :1@N2_:2@C8 6147 0.221 5.84 1.14 23 :1@N3_:2@N7 5967 0.215 5.86 1.05 24 :1@N3_:2@C5 5911 0.213 6.22 0.689 25 :1@C2_:2@N7 3928 0.141 5.78 1.06 26 :1@N2_:2@N7 3424 0.123 5.48 1.32 27 :1@N1_:2@N7 3139 0.113 6.04 0.751 28 :1@N2_:2@C5 3132 0.113 5.56 1.07 29 :1@C2_:2@C5 3128 0.113 6 0.759 30 :1@N3_:2@C6 2621 0.0943 6.3 0.53 31 :1@N3_:2@O6 1551 0.0558 6.38 0.483 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0033 seconds. DATASETS: 9 data sets: [traj] "[traj]" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol RMSD_00001 "RMSD_00001" (double, rms), size is 27794 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 27794 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 27794 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 27794 COM "COM" (double, distance), size is 27794 v_base1 "v_base1" (vector, vector), size is 27794 v_base2 "v_base2" (vector, vector), size is 27794 normalangle "normalangle" (double), size is 27794 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' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 0.4147 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.