CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 13:18:59 | Available memory: 1.223 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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, 60 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 62420 of 62420) Coordinate processing will occur on 62420 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*](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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-62420, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 40 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@O4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@O4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@O4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' Atom ':2@N4' to ':1@N1' Atom ':2@N4' to ':1@C4' Atom ':2@N4' to ':1@O4' Atom ':2@N4' to ':1@N3' Atom ':2@N4' to ':1@C2' Atom ':2@N4' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 62420 frames and processed 62420 frames. TIME: Avg. throughput= 121377.3470 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 32.4119 40 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 51980 0.833 4.52 0.557 2 :2@C5_:1@N1 51857 0.831 4.32 0.5 3 :2@C6_:1@C6 51777 0.829 4.81 0.778 4 :2@C5_:1@C6 51687 0.828 4.37 0.717 5 :2@C5_:1@C2 51569 0.826 4.34 0.637 6 :2@C6_:1@O2 51543 0.826 4.77 0.766 7 :2@C4_:1@N1 51524 0.825 4.64 0.571 8 :2@N1_:1@N1 51512 0.825 4.99 0.567 9 :2@C6_:1@C2 51489 0.825 4.57 0.62 10 :2@C4_:1@C2 51398 0.823 4.38 0.697 11 :2@N1_:1@C2 51252 0.821 4.82 0.688 12 :2@C5_:1@N3 51247 0.821 4.43 0.648 13 :2@C5_:1@O2 51224 0.821 4.73 0.893 14 :2@C4_:1@N3 51190 0.82 4.19 0.659 15 :2@N1_:1@O2 51164 0.82 4.8 0.766 16 :2@N3_:1@C2 51144 0.819 4.64 0.709 17 :2@C5_:1@C5 51122 0.819 4.44 0.801 18 :2@N4_:1@N1 51099 0.819 4.99 0.719 19 :2@C5_:1@C4 51027 0.817 4.54 0.661 20 :2@C6_:1@N3 50922 0.816 4.93 0.715 21 :2@C2_:1@C2 50919 0.816 4.83 0.676 22 :2@N4_:1@N3 50900 0.815 4.19 0.898 23 :2@N4_:1@C4 50885 0.815 4.03 0.729 24 :2@C4_:1@C6 50871 0.815 4.64 0.722 25 :2@C4_:1@C4 50846 0.815 4.25 0.689 26 :2@N3_:1@N1 50827 0.814 5.07 0.656 27 :2@N3_:1@N3 50756 0.813 4.45 0.74 28 :2@C2_:1@O2 50695 0.812 4.8 0.83 29 :2@N4_:1@O4 50599 0.811 4.14 0.797 30 :2@C6_:1@C5 50497 0.809 5.12 0.885 31 :2@N4_:1@C2 50393 0.807 4.65 0.903 32 :2@C5_:1@O4 50301 0.806 5.11 0.718 33 :2@C4_:1@O4 50259 0.805 4.6 0.795 34 :2@N1_:1@N3 50217 0.805 5.14 0.91 35 :2@C6_:1@C4 50148 0.803 5.23 0.808 36 :2@N3_:1@O2 50052 0.802 4.75 0.947 37 :2@C4_:1@O2 49992 0.801 4.69 0.954 38 :2@O2_:1@O2 48114 0.771 5.16 0.859 39 :2@N4_:1@O2 45221 0.724 4.9 0.999 40 :2@C6_:1@O4 42933 0.688 5.73 0.748 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 62420, 'v_base2' size 62420, output size 62420 TIME: Analyses took 0.0085 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 62420 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 62420 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 62420 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 62420 COM "COM" (double, distance), size is 62420 v_base1 "v_base1" (vector, vector), size is 62420 v_base2 "v_base2" (vector, vector), size is 62420 normalangle "normalangle" (double), size is 62420 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.5143 s ( 98.32%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0085 s ( 1.63%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5231 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: 0.8074 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.