
CPPTRAJ: Trajectory Analysis. V13.22
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_
	AmberParm Title: []
Warning: Prmtop missing Box information.
	Radius Set: modified Bondi radii (mbondi)
Warning: [DNA_AMP_wb_vmd.prmtop] ATOMIC_NUMBER not present in topology.
INPUT: Reading Input from STDIN
  [trajin test.dcd 1 10 1]
	[test.dcd] contains 50 frames.
Warning: Box info present in trajectory test.dcd but not in
Warning: associated parm DNA_AMP_wb_vmd.prmtop
Warning: Setting parm box information from trajectory.
  [noprogress]
	Progress bar will not be shown.
  [autoimage]
    AUTOIMAGE: To box center based on center of mass, anchor is first molecule.
  [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
    STRIP: Stripping atoms in mask [:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
  [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
    RMSD: (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), reference is first frame (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), with fitting, mass-weighted.
  [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb]
	Saving frames 1    OUTTRAJ:  [_MMPBSA_complex.pdb] is a PDB file, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1
  [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
	Saving frames 1    OUTTRAJ:  [_MMPBSA_dummycomplex.inpcrd] is an AMBER restart file, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1
  [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-10 nobox]
	Saving frames 1 2 3 4 5 6 7 8 9 10    OUTTRAJ:  [_MMPBSA_complex.mdcrd.0] is an AMBER trajectory, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1 2 3 4 5 6 7 8 9 10
  [strip :28-29]
    STRIP: Stripping atoms in mask [:28-29]
  [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb]
	Saving frames 1    OUTTRAJ:  [_MMPBSA_receptor.pdb] is a PDB file, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1
  [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
	Saving frames 1    OUTTRAJ:  [_MMPBSA_dummyreceptor.inpcrd] is an AMBER restart file, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1
  [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-10 nobox]
	Saving frames 1 2 3 4 5 6 7 8 9 10    OUTTRAJ:  [_MMPBSA_receptor.mdcrd.0] is an AMBER trajectory, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1 2 3 4 5 6 7 8 9 10
  [unstrip]
  [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
    STRIP: Stripping atoms in mask [:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
  [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
    RMSD: (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), reference is first frame (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), with fitting, mass-weighted.
  [strip :1-27]
    STRIP: Stripping atoms in mask [:1-27]
  [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb]
	Saving frames 1    OUTTRAJ:  [_MMPBSA_ligand.pdb] is a PDB file, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1
  [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
	Saving frames 1    OUTTRAJ:  [_MMPBSA_dummyligand.inpcrd] is an AMBER restart file, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1
  [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-10 nobox]
	Saving frames 1 2 3 4 5 6 7 8 9 10    OUTTRAJ:  [_MMPBSA_ligand.mdcrd.0] is an AMBER trajectory, Parm DNA_AMP_wb_vmd.prmtop: Writing frames 1 2 3 4 5 6 7 8 9 10
  [unstrip]
  [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
    STRIP: Stripping atoms in mask [:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
  [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
    RMSD: (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), reference is first frame (!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)), with fitting, mass-weighted.

PARAMETER FILES:
 0: DNA_AMP_wb_vmd.prmtop, 19297 atoms, 6148 res, box: Orthogonal, 6122 mol, 6119 solvent, 10 frames

INPUT TRAJECTORIES:
 0: [test.dcd] is a CHARMM DCD file Little Endian 32 bit, Parm DNA_AMP_wb_vmd.prmtop (Orthogonal box) (reading 10 of 50)
  Coordinate processing will occur on 10 frames.

REFERENCE COORDS:
  No frames defined.

OUTPUT TRAJECTORIES:
  No files.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [DNA_AMP_wb_vmd.prmtop] (20 actions):
  0: [autoimage]
	Anchor molecule is 1
	The following molecules are fixed to anchor: 2 3
	6119 molecules are mobile.
  1: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
	Stripping 18357 atoms.
		Topology DNA_AMP_wb_vmd.prmtop contains 940 atoms.
		                  29 residues.
		                  1016 bonds.
		                  3 molecules.
		                  Box: Orthogonal
  2: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
	Mask [!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)] corresponds to 940 atoms.
  3: [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb]
  4: [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
  5: [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-10 nobox]
  6: [strip :28-29]
	Stripping 70 atoms.
		Topology DNA_AMP_wb_vmd.prmtop contains 870 atoms.
		                  27 residues.
		                  942 bonds.
		                  1 molecules.
		                  Box: Orthogonal
  7: [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb]
  8: [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
  9: [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-10 nobox]
  10: [unstrip]
  11: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
	Stripping 18357 atoms.
		Topology DNA_AMP_wb_vmd.prmtop contains 940 atoms.
		                  29 residues.
		                  1016 bonds.
		                  3 molecules.
		                  Box: Orthogonal
  12: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
	Mask [!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)] corresponds to 940 atoms.
  13: [strip :1-27]
	Stripping 870 atoms.
		Topology DNA_AMP_wb_vmd.prmtop contains 70 atoms.
		                  2 residues.
		                  74 bonds.
		                  2 molecules.
		                  Box: Orthogonal
  14: [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb]
  15: [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
  16: [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-10 nobox]
  17: [unstrip]
  18: [strip :WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+]
	Stripping 18357 atoms.
		Topology DNA_AMP_wb_vmd.prmtop contains 940 atoms.
		                  29 residues.
		                  1016 bonds.
		                  3 molecules.
		                  Box: Orthogonal
  19: [rmsd !(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+) mass first]
	Mask [!(:WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+)] corresponds to 940 atoms.
----- [test.dcd] (1-10, 1) -----

Read 10 frames and processed 10 frames.

ACTION OUTPUT:
  OUTTRAJ: [_MMPBSA_complex.pdb] Wrote 1 frames.
  OUTTRAJ: [_MMPBSA_dummycomplex.inpcrd] Wrote 1 frames.
  OUTTRAJ: [_MMPBSA_complex.mdcrd.0] Wrote 10 frames.
  OUTTRAJ: [_MMPBSA_receptor.pdb] Wrote 1 frames.
  OUTTRAJ: [_MMPBSA_dummyreceptor.inpcrd] Wrote 1 frames.
  OUTTRAJ: [_MMPBSA_receptor.mdcrd.0] Wrote 10 frames.
  OUTTRAJ: [_MMPBSA_ligand.pdb] Wrote 1 frames.
  OUTTRAJ: [_MMPBSA_dummyligand.inpcrd] Wrote 1 frames.
  OUTTRAJ: [_MMPBSA_ligand.mdcrd.0] Wrote 10 frames.

DATASETS:
  3 data sets: 
	RMSD_00000 "RMSD_00000" (double), size is 10
	RMSD_00001 "RMSD_00001" (double), size is 10
	RMSD_00002 "RMSD_00002" (double), size is 10
--------------------------------------------------------------------------------
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.

