CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 13:09:21 | Available memory: 1.217 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.c0] Reading '../ctraj.c0' 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 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,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_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,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base2 :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_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,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, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 46913 of 46913) Coordinate processing will occur on 46913 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base2 :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_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-46913, 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,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 35 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@O4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@O6' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 46913 frames and processed 46913 frames. TIME: Avg. throughput= 76634.0667 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 34.3011 35 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N1 46884 0.999 4.11 0.4 2 :1@C4_:2@C6 46877 0.999 3.9 0.441 3 :1@N9_:2@C6 46848 0.999 4.14 0.388 4 :1@C4_:2@C2 46813 0.998 4.45 0.479 5 :1@N9_:2@N1 46805 0.998 4.7 0.44 6 :1@N9_:2@C5 46765 0.997 4.18 0.427 7 :1@C5_:2@N1 46746 0.996 4.28 0.483 8 :1@C4_:2@N3 46745 0.996 4.57 0.48 9 :1@C6_:2@C2 46738 0.996 3.94 0.531 10 :1@C5_:2@C6 46728 0.996 4.08 0.436 11 :1@C5_:2@C2 46709 0.996 4.26 0.575 12 :1@C5_:2@N3 46689 0.995 4.03 0.502 13 :1@N9_:2@C4 46652 0.994 4.83 0.476 14 :1@C6_:2@O2 46644 0.994 4.3 0.729 15 :1@C8_:2@C6 46613 0.994 4.41 0.487 16 :1@C8_:2@C5 46581 0.993 4.04 0.472 17 :1@N7_:2@C6 46575 0.993 4.42 0.496 18 :1@N7_:2@C5 46565 0.993 3.87 0.453 19 :1@N7_:2@C4 46556 0.992 3.93 0.542 20 :1@C8_:2@C4 46537 0.992 4.5 0.601 21 :1@C4_:2@O2 46508 0.991 5.1 0.592 22 :1@N9_:2@N3 46490 0.991 5.27 0.543 23 :1@N7_:2@N3 46483 0.991 4.49 0.738 24 :1@N9_:2@C2 46480 0.991 5.26 0.537 25 :1@N7_:2@N1 46424 0.99 4.95 0.639 26 :1@C8_:2@O4 46410 0.989 4.78 0.622 27 :1@C8_:2@N1 46403 0.989 5.12 0.603 28 :1@C5_:2@O2 46330 0.988 4.9 0.732 29 :1@O6_:2@O2 46308 0.987 4.53 0.847 30 :1@N7_:2@C2 46177 0.984 4.98 0.77 31 :1@C8_:2@N3 46079 0.982 5.15 0.714 32 :1@C8_:2@C2 45493 0.97 5.45 0.701 33 :1@N9_:2@O2 42733 0.911 5.98 0.56 34 :1@N7_:2@O2 41671 0.888 5.65 0.795 35 :1@C8_:2@O2 35108 0.748 6.07 0.647 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 46913, 'v_base2' size 46913, output size 46913 TIME: Analyses took 0.0034 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 46913 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 46913 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 46913 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 46913 COM "COM" (double, distance), size is 46913 v_base2 "v_base2" (vector, vector), size is 46913 v_base1 "v_base1" (vector, vector), size is 46913 normalangle "normalangle" (double), size is 46913 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.6122 s ( 99.41%) TIME: Action Post : 0.0001 s ( 0.01%) TIME: Analysis : 0.0034 s ( 0.56%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6158 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: 0.7409 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.