CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:18:58 | Available memory: 7.206 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.c3] Reading '../ctraj.c3' 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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8410 of 8410) Coordinate processing will occur on 8410 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.c3 (1-8410, 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 8410 frames and processed 8410 frames. TIME: Avg. throughput= 80384.6227 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 30.4435 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 5443 0.647 5.23 1.02 2 :1@C6_:2@C6 5206 0.619 5.28 1.03 3 :1@O2_:2@C6 5080 0.604 5.17 0.998 4 :1@C2_:2@C6 5073 0.603 5.1 1.04 5 :1@O2_:2@C5 4855 0.577 4.87 1.1 6 :1@N1_:2@N1 4730 0.562 5.45 0.807 7 :1@N1_:2@C5 4722 0.561 4.92 1.01 8 :1@C6_:2@N1 4654 0.553 5.34 0.916 9 :1@C2_:2@C5 4653 0.553 4.72 1.11 10 :1@O2_:2@N1 4624 0.55 5.46 0.965 11 :1@C6_:2@C5 4563 0.543 5.09 1.03 12 :1@C5_:2@C6 4561 0.542 5.22 0.99 13 :1@C2_:2@N1 4558 0.542 5.3 0.886 14 :1@C5_:2@N1 4400 0.523 5.18 0.991 15 :1@N3_:2@C6 4381 0.521 5.05 0.95 16 :1@N3_:2@C5 4220 0.502 4.63 1.06 17 :1@O2_:2@C4 4213 0.501 4.89 1.04 18 :1@N3_:2@N1 4212 0.501 5.15 0.902 19 :1@C4_:2@N1 4179 0.497 5.13 0.914 20 :1@C4_:2@C6 4173 0.496 5.11 0.903 21 :1@C5_:2@C5 4169 0.496 4.99 1 22 :1@C2_:2@C4 4038 0.48 4.63 0.963 23 :1@N1_:2@C4 4007 0.476 5.03 0.813 24 :1@C4_:2@C5 3972 0.472 4.74 0.948 25 :1@C5_:2@C2 3947 0.469 4.98 0.996 26 :1@O2_:2@C2 3913 0.465 5.47 0.992 27 :1@O2_:2@O4 3898 0.463 4.92 0.998 28 :1@C2_:2@C2 3897 0.463 5.21 0.915 29 :1@C6_:2@C2 3883 0.462 5.33 0.825 30 :1@N3_:2@C4 3880 0.461 4.28 1.01 31 :1@O2_:2@N3 3875 0.461 5.21 0.989 32 :1@C2_:2@O4 3874 0.461 4.79 0.881 33 :1@C4_:2@C2 3867 0.46 4.75 1 34 :1@N3_:2@C2 3832 0.456 4.83 0.995 35 :1@C6_:2@C4 3817 0.454 5.06 0.846 36 :1@N1_:2@C2 3801 0.452 5.46 0.72 37 :1@N3_:2@O4 3783 0.45 4.36 0.949 38 :1@C2_:2@N3 3780 0.449 4.89 0.931 39 :1@N4_:2@N1 3779 0.449 5.31 0.843 40 :1@C4_:2@C4 3755 0.446 4.35 0.92 41 :1@C5_:2@C4 3752 0.446 4.75 0.923 42 :1@N3_:2@N3 3742 0.445 4.41 1.03 43 :1@N1_:2@O4 3736 0.444 5.28 0.745 44 :1@C4_:2@N3 3718 0.442 4.36 0.981 45 :1@N4_:2@C2 3710 0.441 4.74 1 46 :1@N1_:2@N3 3702 0.44 5.29 0.732 47 :1@C5_:2@N3 3701 0.44 4.76 0.9 48 :1@C6_:2@N3 3693 0.439 5.22 0.776 49 :1@C4_:2@O4 3663 0.436 4.48 0.916 50 :1@C4_:2@O2 3650 0.434 5.03 0.946 51 :1@N4_:2@C6 3648 0.434 5.45 0.762 52 :1@N4_:2@C5 3646 0.434 5.07 0.828 53 :1@C5_:2@O2 3645 0.433 5.24 0.963 54 :1@N4_:2@N3 3636 0.432 4.32 1.01 55 :1@N4_:2@O2 3619 0.43 4.88 1.02 56 :1@N4_:2@C4 3612 0.429 4.46 0.894 57 :1@C6_:2@O4 3571 0.425 5.35 0.909 58 :1@N3_:2@O2 3563 0.424 5.21 0.958 59 :1@N4_:2@O4 3552 0.422 4.48 0.942 60 :1@C5_:2@O4 3551 0.422 4.96 0.985 61 :1@C6_:2@O2 3371 0.401 5.69 0.799 62 :1@C2_:2@O2 3316 0.394 5.62 0.878 63 :1@N1_:2@O2 3161 0.376 5.91 0.715 64 :1@O2_:2@O2 2805 0.334 5.66 0.972 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 8410, 'v_base2' size 8410, output size 8410 TIME: Analyses took 0.0011 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 8410 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8410 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8410 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8410 COM "COM" (double, distance), size is 8410 v_base1 "v_base1" (vector, vector), size is 8410 v_base2 "v_base2" (vector, vector), size is 8410 normalangle "normalangle" (double), size is 8410 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.1046 s ( 98.64%) TIME: Action Post : 0.0002 s ( 0.21%) TIME: Analysis : 0.0011 s ( 1.06%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1061 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: 0.1553 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.