CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 18:09:58 | Available memory: 52480.3 MB INPUT: Reading Input from file 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-] 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*), with fitting. [nativecontacts :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,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,N4,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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,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,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,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: 0: [traj] 'noWAt.topo.hmr', 61 atoms, 2 res, box: Orthogonal, 1 mol, 38514 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 38514 of 38514) Coordinate processing will occur on 38514 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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,N4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,N4,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,N4,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,N4,H41,H42,N3,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,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c4 (1-38514, 1) ----- 0% 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,N4,N3,C2,O2] corresponds to 8 atoms. Setup 37 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@N4' 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@N4' 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@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 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@C4' 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@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 38514 frames and processed 38514 frames. TIME: Trajectory processing: 0.1723 s TIME: Avg. throughput= 223469.0680 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 8.21545 37 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 21757 0.565 6.17 0.495 2 :1@N1_:2@C5 21567 0.56 5.87 0.634 3 :1@C6_:2@C5 19471 0.506 5.82 0.895 4 :1@C6_:2@C6 17425 0.452 6.11 0.72 5 :1@N1_:2@C4 15214 0.395 5.93 0.719 6 :1@C6_:2@C4 14180 0.368 5.7 0.94 7 :1@C6_:2@N4 13561 0.352 5.53 1.06 8 :1@N1_:2@N4 13529 0.351 5.83 0.814 9 :1@N1_:2@N1 11626 0.302 6.39 0.418 10 :1@C2_:2@C4 10887 0.283 6.07 0.663 11 :1@C5_:2@N4 10518 0.273 5.5 1.1 12 :1@C6_:2@N1 10057 0.261 6.23 0.56 13 :1@C6_:2@N3 10049 0.261 5.77 0.826 14 :1@C5_:2@C4 9586 0.249 5.73 0.93 15 :1@N1_:2@N3 9500 0.247 5.93 0.688 16 :1@C6_:2@C2 8833 0.229 6.1 0.632 17 :1@N1_:2@C2 8106 0.21 6.16 0.566 18 :1@C5_:2@N3 7396 0.192 5.89 0.743 19 :1@C2_:2@N3 6788 0.176 6.11 0.644 20 :1@O2_:2@N3 6615 0.172 5.97 0.812 21 :1@O2_:2@N1 6227 0.162 6.29 0.586 22 :1@C6_:2@O2 5509 0.143 6.21 0.633 23 :1@C5_:2@C2 5484 0.142 6.26 0.544 24 :1@O2_:2@C2 5397 0.14 6.21 0.628 25 :1@C2_:2@N1 5391 0.14 6.52 0.387 26 :1@C2_:2@C2 5053 0.131 6.32 0.501 27 :1@N1_:2@O2 4873 0.127 6.18 0.552 28 :1@C5_:2@N1 4739 0.123 6.31 0.528 29 :1@C4_:2@N3 4626 0.12 6.28 0.514 30 :1@N3_:2@N3 4291 0.111 6.28 0.563 31 :1@O2_:2@O2 3426 0.089 6.31 0.557 32 :1@C5_:2@O2 3285 0.0853 6.33 0.59 33 :1@C2_:2@O2 3278 0.0851 6.32 0.499 34 :1@N3_:2@C2 2403 0.0624 6.49 0.393 35 :1@C4_:2@C2 2348 0.061 6.54 0.353 36 :1@N3_:2@O2 1798 0.0467 6.47 0.425 37 :1@C4_:2@O2 1617 0.042 6.49 0.432 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0017 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 38514 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 38514 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 38514 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 38514 COM "COM" (double, distance), size is 38514 v_base1 "v_base1" (vector), size is 38514 v_base2 "v_base2" (vector), size is 38514 normalangle "normalangle" (double), size is 38514 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.2739 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.