CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 10:59:38 | Available memory: 87374.7 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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_base2 :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_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3297 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0003 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 61 atoms, 2 res, box: Orthogonal, 1 mol 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_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. 6: [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. ----- traj.1.01 (1-50000, 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 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@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@C6' Atom ':1@C5' to ':2@C5' 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@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' 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@N4' 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@N4' 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@N4' 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@N4' 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 50000 frames and processed 50000 frames. TIME: Trajectory processing: 31.7502 s TIME: Avg. throughput= 1574.7955 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 29.7815 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 28802 0.576 4.95 0.859 2 :1@C6_:2@C6 27729 0.555 4.93 1.04 3 :1@C2_:2@C6 27557 0.551 4.92 0.944 4 :1@N1_:2@C5 27397 0.548 4.9 0.849 5 :1@N1_:2@N1 26849 0.537 5.26 0.763 6 :1@C6_:2@C5 26606 0.532 4.78 1.02 7 :1@O2_:2@C6 26543 0.531 5.05 1.1 8 :1@C2_:2@N1 26382 0.528 5.09 0.833 9 :1@C2_:2@C5 26354 0.527 4.86 1.07 10 :1@N3_:2@C6 25930 0.519 5.02 0.903 11 :1@C5_:2@C6 25487 0.51 4.94 1.03 12 :1@O2_:2@N1 25473 0.509 5.24 0.925 13 :1@N3_:2@C5 25118 0.502 4.88 1.05 14 :1@C5_:2@C5 25038 0.501 4.73 1.04 15 :1@C4_:2@C6 25038 0.501 5.07 0.844 16 :1@N1_:2@C4 25035 0.501 5.28 0.71 17 :1@C6_:2@N1 24998 0.5 5.11 0.987 18 :1@N3_:2@N1 24947 0.499 5 0.896 19 :1@C4_:2@C5 24833 0.497 4.89 0.913 20 :1@C2_:2@C2 24311 0.486 5.25 0.809 21 :1@C2_:2@C4 24215 0.484 5.06 0.983 22 :1@O2_:2@C5 24117 0.482 4.92 1.27 23 :1@N3_:2@C4 23954 0.479 4.84 1.07 24 :1@C4_:2@N1 23925 0.478 4.96 0.939 25 :1@C6_:2@C4 23810 0.476 4.96 0.897 26 :1@C4_:2@C4 23687 0.474 4.7 0.946 27 :1@C5_:2@N1 23678 0.474 4.94 1.09 28 :1@N3_:2@C2 23649 0.473 4.91 0.917 29 :1@C2_:2@N3 23532 0.471 5.27 0.866 30 :1@N1_:2@C2 23456 0.469 5.48 0.683 31 :1@N3_:2@N3 23405 0.468 4.89 0.978 32 :1@N1_:2@N3 23175 0.464 5.54 0.672 33 :1@C5_:2@C4 23037 0.461 4.62 1 34 :1@N1_:2@N4 22922 0.458 5.64 0.72 35 :1@O2_:2@C2 22878 0.458 5.43 0.908 36 :1@C4_:2@C2 22786 0.456 4.74 0.975 37 :1@C4_:2@N3 22699 0.454 4.64 0.933 38 :1@C4_:2@N4 22642 0.453 4.9 1.02 39 :1@N4_:2@C5 22521 0.45 5.26 0.84 40 :1@C6_:2@N4 22287 0.446 5.25 0.862 41 :1@N4_:2@C4 22234 0.445 4.83 0.947 42 :1@N4_:2@C6 22169 0.443 5.48 0.734 43 :1@C6_:2@C2 22062 0.441 5.2 0.92 44 :1@C5_:2@N4 22053 0.441 4.82 0.994 45 :1@C6_:2@N3 21986 0.44 5.17 0.883 46 :1@C5_:2@C2 21980 0.44 4.82 1.09 47 :1@C5_:2@N3 21869 0.437 4.7 1.04 48 :1@N4_:2@N3 21818 0.436 4.62 0.978 49 :1@N3_:2@O2 21758 0.435 5.13 0.884 50 :1@N4_:2@N1 21573 0.431 5.2 0.864 51 :1@N4_:2@C2 21484 0.43 4.76 0.986 52 :1@C2_:2@O2 21468 0.429 5.57 0.781 53 :1@N3_:2@N4 21342 0.427 4.95 1.1 54 :1@N4_:2@N4 21224 0.424 4.87 1.08 55 :1@C4_:2@O2 21001 0.42 4.91 0.976 56 :1@C2_:2@N4 20673 0.413 5.22 0.951 57 :1@O2_:2@C4 20523 0.41 5.01 1.12 58 :1@O2_:2@N3 20261 0.405 5.31 0.966 59 :1@N4_:2@O2 20252 0.405 4.76 1.07 60 :1@O2_:2@O2 19622 0.392 5.73 0.835 61 :1@N1_:2@O2 19621 0.392 5.83 0.753 62 :1@C5_:2@O2 19570 0.391 5.05 1.04 63 :1@C6_:2@O2 18590 0.372 5.5 0.894 64 :1@O2_:2@N4 17140 0.343 5.06 1.09 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0025 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base2 "v_base2" (vector), size is 50000 v_base1 "v_base1" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 32.4212 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.