
CPPTRAJ: Trajectory Analysis. V16.00b
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| Date/time: 07/27/15  11:52:44
| Available memory: 3807.43 MB

INPUT: Reading Input from file traj.in
  [parm rna_a_form_dup.pdb]
	Reading 'rna_a_form_dup.pdb' as PDB File
	rna_a_form_dup.pdb: determining bond info from distances.
Warning: rna_a_form_dup.pdb: Determining default bond distances from element types.
  [trajin rna_a_form_dup.pdb]
	Reading 'rna_a_form_dup.pdb' as PDB
  [nastruct naout na.out]
    NAstruct: Scanning all NA residues
	Base pair parameters written to BP.na.out
	Base pair step parameters written to BPstep.na.out
	Helical parameters written to Helix.na.out
	Hydrogen bond cutoff for determining base pairs is 3.50 Angstroms.
	Base reference axes origin cutoff for determining base pairs is 2.50 Angstroms.
	Using first frame to determine base pairing.
	Calculating sugar pucker using Altona & Sundaralingam method.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: 'rna_a_form_dup.pdb', 250 atoms, 8 res, box: None, 2 mol, 1 frames

INPUT TRAJECTORIES:
 0: 'rna_a_form_dup.pdb' is a PDB file, Parm rna_a_form_dup.pdb (reading 1 of 1)
  Coordinate processing will occur on 1 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'rna_a_form_dup.pdb' (1 actions):
  0: [nastruct naout na.out]
	Set up 8 bases.
----- rna_a_form_dup.pdb (1-1, 1) -----
100% Complete.

Read 1 frames and processed 1 frames.
TIME: Trajectory processing: 0.0057 s
TIME: Avg. throughput= 175.1620 frames / second.

ACTION OUTPUT:
	Base pair output file BP.na.out; 1 frames, 4 base pairs.
	Base pair step output file BPstep.na.out, Helix output file Helix.na.out; 1 frames, 3 base pair steps.

DATASETS:
  80 data sets:
	NA_00000[pucker]:1 "1A" (float, pucker(pucker)), size is 1
	NA_00000[pucker]:8 "8U" (float, pucker(pucker)), size is 1
	NA_00000[shear]:1 "1A8U" (float), size is 1
	NA_00000[stretch]:1 "1A8U" (float), size is 1
	NA_00000[stagger]:1 "1A8U" (float), size is 1
	NA_00000[buckle]:1 "1A8U" (float), size is 1
	NA_00000[prop]:1 "1A8U" (float), size is 1
	NA_00000[open]:1 "1A8U" (float), size is 1
	NA_00000[hb]:1 "1A8U" (integer), size is 1
	NA_00000[major]:1 "1A8U" (float), size is 1
	NA_00000[minor]:1 "1A8U" (float), size is 1
	NA_00000[pucker]:2 "2A" (float, pucker(pucker)), size is 1
	NA_00000[pucker]:7 "7U" (float, pucker(pucker)), size is 1
	NA_00000[shear]:2 "2A7U" (float), size is 1
	NA_00000[stretch]:2 "2A7U" (float), size is 1
	NA_00000[stagger]:2 "2A7U" (float), size is 1
	NA_00000[buckle]:2 "2A7U" (float), size is 1
	NA_00000[prop]:2 "2A7U" (float), size is 1
	NA_00000[open]:2 "2A7U" (float), size is 1
	NA_00000[hb]:2 "2A7U" (integer), size is 1
	NA_00000[major]:2 "2A7U" (float), size is 1
	NA_00000[minor]:2 "2A7U" (float), size is 1
	NA_00000[pucker]:3 "3U" (float, pucker(pucker)), size is 1
	NA_00000[pucker]:6 "6A" (float, pucker(pucker)), size is 1
	NA_00000[shear]:3 "3U6A" (float), size is 1
	NA_00000[stretch]:3 "3U6A" (float), size is 1
	NA_00000[stagger]:3 "3U6A" (float), size is 1
	NA_00000[buckle]:3 "3U6A" (float), size is 1
	NA_00000[prop]:3 "3U6A" (float), size is 1
	NA_00000[open]:3 "3U6A" (float), size is 1
	NA_00000[hb]:3 "3U6A" (integer), size is 1
	NA_00000[major]:3 "3U6A" (float), size is 1
	NA_00000[minor]:3 "3U6A" (float), size is 1
	NA_00000[pucker]:4 "4U" (float, pucker(pucker)), size is 1
	NA_00000[pucker]:5 "5A" (float, pucker(pucker)), size is 1
	NA_00000[shear]:4 "4U5A" (float), size is 1
	NA_00000[stretch]:4 "4U5A" (float), size is 1
	NA_00000[stagger]:4 "4U5A" (float), size is 1
	NA_00000[buckle]:4 "4U5A" (float), size is 1
	NA_00000[prop]:4 "4U5A" (float), size is 1
	NA_00000[open]:4 "4U5A" (float), size is 1
	NA_00000[hb]:4 "4U5A" (integer), size is 1
	NA_00000[major]:4 "4U5A" (float), size is 1
	NA_00000[minor]:4 "4U5A" (float), size is 1
	NA_00000[shift]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[slide]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[rise]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[tilt]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[roll]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[twist]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[xdisp]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[ydisp]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[hrise]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[incl]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[tip]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[htwist]:1 "1A8U-2A7U" (float), size is 1
	NA_00000[shift]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[slide]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[rise]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[tilt]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[roll]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[twist]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[xdisp]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[ydisp]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[hrise]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[incl]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[tip]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[htwist]:2 "2A7U-3U6A" (float), size is 1
	NA_00000[shift]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[slide]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[rise]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[tilt]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[roll]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[twist]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[xdisp]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[ydisp]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[hrise]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[incl]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[tip]:3 "3U6A-4U5A" (float), size is 1
	NA_00000[htwist]:3 "3U6A-4U5A" (float), size is 1

DATAFILES:
  BP.na.out (Base Pair)
  BPstep.na.out (Base Pair Step)
  Helix.na.out (Helix)
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.0239 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.

