CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 10:28:00 | Available memory: 3.622 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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55857 of 55857) Coordinate processing will occur on 55857 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.c0 (1-55857, 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 55857 frames and processed 55857 frames. TIME: Avg. throughput= 120362.5292 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 63.1021 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@N1 55857 1 4.48 0.351 2 :1@C4_:2@N1 55852 1 4.28 0.478 3 :1@C4_:2@C2 55846 1 3.99 0.477 4 :1@C6_:2@N1 55846 1 4.56 0.471 5 :1@N1_:2@C6 55839 1 4.14 0.375 6 :1@C6_:2@C6 55837 1 4.06 0.421 7 :1@C5_:2@N1 55833 1 4.47 0.548 8 :1@C5_:2@C6 55827 0.999 4.18 0.473 9 :1@C2_:2@N1 55822 0.999 4.29 0.512 10 :1@C4_:2@N3 55818 0.999 3.78 0.45 11 :1@N1_:2@C5 55816 0.999 4.33 0.438 12 :1@C4_:2@C6 55816 0.999 4.37 0.477 13 :1@C5_:2@C2 55814 0.999 4.4 0.603 14 :1@N1_:2@C2 55814 0.999 4.96 0.432 15 :1@N4_:2@C2 55809 0.999 4.09 0.572 16 :1@C2_:2@C6 55805 0.999 4.35 0.538 17 :1@C6_:2@C5 55804 0.999 3.87 0.447 18 :1@N3_:2@N1 55801 0.999 4.19 0.532 19 :1@N4_:2@N1 55790 0.999 4.75 0.568 20 :1@C6_:2@C2 55789 0.999 4.87 0.539 21 :1@N1_:2@C4 55787 0.999 4.87 0.468 22 :1@C5_:2@N3 55778 0.999 4.02 0.529 23 :1@C5_:2@C5 55774 0.999 3.78 0.48 24 :1@C6_:2@C4 55767 0.998 4.25 0.482 25 :1@N3_:2@C6 55766 0.998 4.46 0.56 26 :1@N1_:2@N3 55766 0.998 5.1 0.473 27 :1@N4_:2@N3 55761 0.998 3.71 0.506 28 :1@C6_:2@N3 55760 0.998 4.69 0.527 29 :1@C5_:2@C4 55746 0.998 3.71 0.468 30 :1@N3_:2@C2 55745 0.998 4.08 0.55 31 :1@C4_:2@C4 55740 0.998 3.89 0.522 32 :1@C4_:2@C5 55739 0.998 4.18 0.541 33 :1@N3_:2@N3 55724 0.998 4.24 0.626 34 :1@C4_:2@O2 55717 0.997 4.45 0.637 35 :1@C2_:2@C5 55689 0.997 4.67 0.609 36 :1@C2_:2@C2 55680 0.997 4.58 0.549 37 :1@N4_:2@O2 55659 0.996 4.33 0.753 38 :1@N4_:2@C4 55625 0.996 4.02 0.607 39 :1@C2_:2@N3 55612 0.996 4.88 0.606 40 :1@N3_:2@C5 55609 0.996 4.59 0.651 41 :1@N4_:2@C6 55605 0.995 5.01 0.528 42 :1@C5_:2@O4 55581 0.995 3.98 0.58 43 :1@C6_:2@O4 55568 0.995 4.68 0.567 44 :1@N3_:2@C4 55554 0.995 4.52 0.686 45 :1@C2_:2@C4 55515 0.994 4.98 0.632 46 :1@N4_:2@C5 55510 0.994 4.68 0.603 47 :1@C4_:2@O4 55498 0.994 4.29 0.662 48 :1@N3_:2@O2 55481 0.993 4.39 0.623 49 :1@O2_:2@C6 55426 0.992 4.93 0.673 50 :1@O2_:2@N1 55340 0.991 4.71 0.694 51 :1@C5_:2@O2 55307 0.99 5.11 0.736 52 :1@N4_:2@O4 55283 0.99 4.21 0.771 53 :1@N1_:2@O4 55209 0.988 5.5 0.532 54 :1@C2_:2@O2 55121 0.987 5.02 0.597 55 :1@N1_:2@O2 54891 0.983 5.64 0.503 56 :1@O2_:2@C2 54746 0.98 5.09 0.724 57 :1@N3_:2@O4 54415 0.974 5.09 0.761 58 :1@C6_:2@O2 54378 0.974 5.65 0.617 59 :1@O2_:2@C5 54180 0.97 5.44 0.711 60 :1@C2_:2@O4 53132 0.951 5.63 0.658 61 :1@O2_:2@O2 53020 0.949 5.33 0.733 62 :1@O2_:2@N3 52893 0.947 5.57 0.709 63 :1@O2_:2@C4 51148 0.916 5.75 0.706 64 :1@O2_:2@O4 35013 0.627 6.18 0.704 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 55857, 'v_base2' size 55857, output size 55857 TIME: Analyses took 0.0076 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 55857 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 55857 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 55857 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 55857 COM "COM" (double, distance), size is 55857 v_base1 "v_base1" (vector, vector), size is 55857 v_base2 "v_base2" (vector, vector), size is 55857 normalangle "normalangle" (double), size is 55857 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.4641 s ( 98.33%) TIME: Action Post : 0.0002 s ( 0.04%) TIME: Analysis : 0.0076 s ( 1.61%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4720 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: 0.7188 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.