CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:15:51 | Available memory: 1.720 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 :1@N1,C6,C5,C4,N4,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,N4,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_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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :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, 60 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 6024 of 6024) Coordinate processing will occur on 6024 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 :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 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,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :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.c4 (1-6024, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 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@C6' to ':2@O2' Atom ':1@C5' to ':2@N1' 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@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' 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@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@N4' to ':2@N1' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@O2' 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@N3' to ':2@O2' 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@C2' to ':2@O2' 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 6024 frames and processed 6024 frames. TIME: Avg. throughput= 17494.1338 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 42.5083 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 5112 0.849 5.1 0.945 2 :1@C2_:2@C6 4895 0.813 5.06 1.02 3 :1@C6_:2@C6 4837 0.803 5.1 0.95 4 :1@C6_:2@N1 4755 0.789 5.33 0.885 5 :1@N1_:2@N1 4720 0.784 5.45 0.801 6 :1@C2_:2@C5 4582 0.761 4.66 1.05 7 :1@C5_:2@N1 4568 0.758 5.21 0.988 8 :1@N1_:2@C5 4530 0.752 4.77 0.898 9 :1@C5_:2@C6 4516 0.75 5.13 0.935 10 :1@O2_:2@C5 4469 0.742 4.78 1.07 11 :1@O2_:2@C6 4454 0.739 5.06 0.98 12 :1@N3_:2@C6 4417 0.733 5.06 0.962 13 :1@C6_:2@C5 4365 0.725 4.89 0.956 14 :1@N3_:2@C5 4362 0.724 4.66 1.05 15 :1@C2_:2@N1 4336 0.72 5.25 0.87 16 :1@C4_:2@C6 4314 0.716 5.14 0.904 17 :1@C4_:2@N1 4199 0.697 5.14 0.919 18 :1@C2_:2@C4 4154 0.69 4.67 0.978 19 :1@C5_:2@C5 4151 0.689 4.85 0.939 20 :1@N3_:2@N1 4145 0.688 5.13 0.892 21 :1@C4_:2@C5 4144 0.688 4.74 0.923 22 :1@C5_:2@C2 4138 0.687 5.04 1.02 23 :1@N1_:2@C4 4098 0.68 5 0.761 24 :1@N3_:2@C4 4077 0.677 4.38 1.08 25 :1@C6_:2@C2 4075 0.676 5.37 0.821 26 :1@O2_:2@N1 4033 0.669 5.37 0.96 27 :1@C2_:2@O4 4001 0.664 4.81 0.882 28 :1@C4_:2@C4 3983 0.661 4.41 0.937 29 :1@N3_:2@O4 3978 0.66 4.43 0.973 30 :1@C6_:2@C4 3970 0.659 4.99 0.828 31 :1@O2_:2@C4 3962 0.658 4.81 0.994 32 :1@C5_:2@C4 3927 0.652 4.7 0.886 33 :1@C5_:2@N3 3910 0.649 4.8 0.889 34 :1@C4_:2@O4 3891 0.646 4.5 0.893 35 :1@C6_:2@N3 3883 0.645 5.22 0.756 36 :1@C4_:2@N3 3875 0.643 4.45 1.06 37 :1@N1_:2@O4 3875 0.643 5.25 0.721 38 :1@C4_:2@C2 3859 0.641 4.75 1 39 :1@N1_:2@N3 3846 0.638 5.33 0.744 40 :1@N1_:2@C2 3842 0.638 5.49 0.731 41 :1@N4_:2@C4 3824 0.635 4.54 0.937 42 :1@N4_:2@C5 3821 0.634 5.09 0.824 43 :1@O2_:2@O4 3818 0.634 4.9 0.995 44 :1@N3_:2@C2 3807 0.632 4.83 0.995 45 :1@N4_:2@O4 3799 0.631 4.53 0.946 46 :1@C2_:2@C2 3797 0.63 5.18 0.898 47 :1@N4_:2@N1 3781 0.628 5.32 0.844 48 :1@C2_:2@N3 3764 0.625 4.89 0.929 49 :1@N3_:2@N3 3754 0.623 4.42 1.04 50 :1@N4_:2@C6 3750 0.623 5.48 0.775 51 :1@C5_:2@O4 3742 0.621 4.87 0.991 52 :1@C6_:2@O4 3732 0.62 5.25 0.932 53 :1@N4_:2@C2 3707 0.615 4.74 1 54 :1@N4_:2@N3 3704 0.615 4.36 1.06 55 :1@O2_:2@N3 3642 0.605 5.14 0.958 56 :1@C5_:2@O2 3641 0.604 5.24 0.966 57 :1@C4_:2@O2 3633 0.603 5.02 0.944 58 :1@O2_:2@C2 3613 0.6 5.42 0.988 59 :1@N4_:2@O2 3611 0.599 4.88 1.02 60 :1@N3_:2@O2 3535 0.587 5.21 0.956 61 :1@C6_:2@O2 3420 0.568 5.7 0.808 62 :1@C2_:2@O2 3238 0.538 5.61 0.874 63 :1@N1_:2@O2 3098 0.514 5.91 0.714 64 :1@O2_:2@O2 2591 0.43 5.63 0.972 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 6024, 'v_base2' size 6024, output size 6024 TIME: Analyses took 0.0008 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 6024 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 6024 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 6024 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 6024 COM "COM" (double, distance), size is 6024 v_base1 "v_base1" (vector, vector), size is 6024 v_base2 "v_base2" (vector, vector), size is 6024 normalangle "normalangle" (double), size is 6024 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0002 s ( 0.06%) TIME: Trajectory Process : 0.3443 s ( 99.64%) TIME: Action Post : 0.0002 s ( 0.06%) TIME: Analysis : 0.0008 s ( 0.23%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.3456 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: 4.4012 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.