CPPTRAJ: Trajectory Analysis. V18.01 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/30/18 08:49:24 | Available memory: 4.913 GB INPUT: Reading input from 'cpptraj.in' [parm near_parallel_ringtest.pdb] Reading 'near_parallel_ringtest.pdb' as PDB File Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Warning: CONECT record has more than 4 bonds. Only using first 4 bonds. Determining bond info from distances. Warning: Bond length not found for ?? - N, using default= 1.600000 Warning: Bond length not found for ?? - C, using default= 1.600000 Warning: near_parallel_ringtest.pdb: Determining default bond distances from element types. [trajin near_parallel_ringtest.pdb] Reading 'near_parallel_ringtest.pdb' as PDB [vector name1 corrplane :13@CG,ND1,CD2,CE1,NE2] VECTOR: Type CorrPlane, mask [:13@CG,ND1,CD2,CE1,NE2] [vector name2 corrplane :14@CG,ND1,CD2,CE1,NE2] VECTOR: Type CorrPlane, mask [:14@CG,ND1,CD2,CE1,NE2] [vectormath vec1 name1 vec2 name2 dotangle out name1_name2_angle.dat] VECTORMATH: Calculating Angle from dot product of vectors name1 and name2 Vectors will be normalized. Results are written to name1_name2_angle.dat [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: near_parallel_ringtest.pdb, 262 atoms, 18 res, box: None, 2 mol INPUT TRAJECTORIES (1 total): 0: 'near_parallel_ringtest.pdb' is a PDB file, Parm near_parallel_ringtest.pdb (reading 1 of 1) Coordinate processing will occur on 1 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'near_parallel_ringtest.pdb' (2 actions): 0: [vector name1 corrplane :13@CG,ND1,CD2,CE1,NE2] Mask [:13@CG,ND1,CD2,CE1,NE2] corresponds to 5 atoms. 1: [vector name2 corrplane :14@CG,ND1,CD2,CE1,NE2] Mask [:14@CG,ND1,CD2,CE1,NE2] corresponds to 5 atoms. ----- near_parallel_ringtest.pdb (1-1, 1) ----- 100% Complete. Read 1 frames and processed 1 frames. TIME: Avg. throughput= 2801.1204 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [vectormath vec1 name1 vec2 name2 dotangle out name1_name2_angle.dat] 'name1' size 1, 'name2' size 1, output size 1 TIME: Analyses took 0.0000 seconds. DATASETS (3 total): name1 "name1" (vector, vector), size is 1 name2 "name2" (vector, vector), size is 1 Angle_00003 "Angle_00003" (double), size is 1 DATAFILES (1 total): name1_name2_angle.dat (Standard Data File): Angle_00003 RUN TIMING: TIME: Init : 0.0000 s ( 5.02%) TIME: Trajectory Process : 0.0004 s ( 68.92%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.58%) TIME: Data File Write : 0.0001 s ( 22.78%) TIME: Other : 0.0000 s ( 0.03%) TIME: Run Total 0.0005 s ---------- RUN END --------------------------------------------------- [writedata vecs.mol2 name1 name2 vectraj trajfmt mol2] Writing sets to vecs.mol2, format 'Vector pseudo-traj' name1 name2 Warning: Could not determine atomic number from name [VXYZ] Warning: Could not determine atomic number from name [VXYZ] Writing 'vecs.mol2' as Mol2 TIME: Total execution time: 0.0036 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.