CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:19:34 | Available memory: 1.242 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c4] Reading '../ctraj.c4' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [nativecontacts :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':1@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_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 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [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] [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1888 of 1888) Coordinate processing will occur on 1888 frames. 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*](40) Reference mask: [:1,2&!@H*](40) 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 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [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. 6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c4 (1-1888, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 37 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@O6' to ':1@N1' Atom ':2@O6' to ':1@C6' Atom ':2@O6' to ':1@C2' Atom ':2@O6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N2' to ':1@N1' Atom ':2@N2' to ':1@C6' Atom ':2@N2' to ':1@N3' Atom ':2@N2' to ':1@C2' Atom ':2@N2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 1888 frames and processed 1888 frames. TIME: Avg. throughput= 76545.7125 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 6.60222 37 # Contact Nframes Frac. Avg Stdev 1 :2@N3_:1@O2 859 0.455 6.17 0.746 2 :2@N2_:1@N1 837 0.443 6.24 0.729 3 :2@N3_:1@N1 827 0.438 6.43 0.606 4 :2@C4_:1@O2 668 0.354 6.14 0.662 5 :2@N9_:1@O2 644 0.341 5.99 0.802 6 :2@C2_:1@N1 580 0.307 6.4 0.771 7 :2@N2_:1@O2 575 0.305 5.97 1.01 8 :2@C2_:1@O2 537 0.284 6.1 0.852 9 :2@N3_:1@C2 472 0.25 6.36 0.731 10 :2@C5_:1@O2 441 0.234 6.08 0.682 11 :2@N9_:1@N1 430 0.228 6.38 0.47 12 :2@C4_:1@N1 404 0.214 6.42 0.629 13 :2@N7_:1@N1 366 0.194 6.2 0.598 14 :2@N7_:1@O2 346 0.183 5.64 1.23 15 :2@N2_:1@C2 342 0.181 5.96 0.995 16 :2@C4_:1@C2 341 0.181 6.41 0.541 17 :2@C5_:1@N1 328 0.174 6.34 0.514 18 :2@C6_:1@O2 325 0.172 6.28 0.536 19 :2@N2_:1@C6 317 0.168 6.17 0.965 20 :2@N1_:1@O2 311 0.165 6.11 0.731 21 :2@C2_:1@C2 258 0.137 6.06 0.897 22 :2@C5_:1@C2 247 0.131 6.37 0.444 23 :2@N1_:1@N1 210 0.111 6.02 0.855 24 :2@C6_:1@N1 195 0.103 6.15 0.637 25 :2@O6_:1@O2 192 0.102 6.35 0.503 26 :2@N1_:1@C2 160 0.0847 6.07 0.711 27 :2@C6_:1@C2 148 0.0784 6.41 0.487 28 :2@O6_:1@N1 145 0.0768 6.29 0.512 29 :2@C2_:1@C6 142 0.0752 5.81 1.02 30 :2@N2_:1@N3 138 0.0731 5.75 0.977 31 :2@N1_:1@C6 128 0.0678 5.93 0.923 32 :2@C6_:1@C6 105 0.0556 6.14 0.637 33 :2@C5_:1@C6 105 0.0556 6.33 0.553 34 :2@C2_:1@N3 97 0.0514 5.94 0.778 35 :2@O6_:1@C2 91 0.0482 6.56 0.362 36 :2@O6_:1@C6 90 0.0477 6.34 0.473 37 :2@N1_:1@N3 64 0.0339 6.2 0.528 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 1888, 'v_base2' size 1888, output size 1888 TIME: Analyses took 0.0002 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 1888 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 1888 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 1888 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 1888 COM "COM" (double, distance), size is 1888 v_base2 "v_base2" (vector, vector), size is 1888 v_base1 "v_base1" (vector, vector), size is 1888 normalangle "normalangle" (double), size is 1888 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.12%) TIME: Trajectory Process : 0.0247 s ( 98.24%) TIME: Action Post : 0.0001 s ( 0.53%) TIME: Analysis : 0.0002 s ( 0.93%) TIME: Data File Write : 0.0000 s ( 0.09%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.0251 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.0453 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.