_MMPBSA_cpptraj_entropy.out

gistfile1.txt

CPPTRAJ: Trajectory Analysis. V15.00
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| Date/time: 06/20/15  14:56:29
| Available memory: 4313.49 MB

	Reading 'com.top' as Amber Topology
INPUT: Reading Input from file _MMPBSA_cpptrajentropy.in
  [trajin _MMPBSA_complex.mdcrd]
	Reading '_MMPBSA_complex.mdcrd' as Amber Trajectory
  [reference _MMPBSA_avgcomplex.pdb]
	Reading '_MMPBSA_avgcomplex.pdb' as PDB
  [rms mass reference :1-247]
	Reference mask: [:1-247](3907)
    RMSD: (:1-247), reference is "_MMPBSA_avgcomplex.pdb" (:1-247), with fitting, mass-weighted.
  [matrix mwcovar name comp.matrix :1-247]
    MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
	Matrix data set is 'comp.matrix'
	Start: 1  Stop: Final frame
	Mask1 is ':1-247'
  [analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce]
	Changed DataFile '_MMPBSA_complex_entropy.out' type to Evecs file for set Modes_00003
    DIAGMATRIX: Diagonalizing matrix comp.matrix and writing modes to _MMPBSA_complex_entropy.out
	Calculating 0 eigenvectors and thermodynamic data at 298.15 K, output to STDOUT
  [rms mass reference :1-246]
	Reference mask: [:1-246](3817)
    RMSD: (:1-246), reference is "_MMPBSA_avgcomplex.pdb" (:1-246), with fitting, mass-weighted.
  [matrix mwcovar name rec.matrix :1-246]
    MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
	Matrix data set is 'rec.matrix'
	Start: 1  Stop: Final frame
	Mask1 is ':1-246'
  [analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce]
	Changed DataFile '_MMPBSA_receptor_entropy.out' type to Evecs file for set Modes_00006
    DIAGMATRIX: Diagonalizing matrix rec.matrix and writing modes to _MMPBSA_receptor_entropy.out
	Calculating 0 eigenvectors and thermodynamic data at 298.15 K, output to STDOUT
  [rms mass reference :247]
	Reference mask: [:247](90)
    RMSD: (:247), reference is "_MMPBSA_avgcomplex.pdb" (:247), with fitting, mass-weighted.
  [matrix mwcovar name lig.matrix :247]
    MATRIX: Calculating mass-weighted covariance matrix, output is by atom.
	Matrix data set is 'lig.matrix'
	Start: 1  Stop: Final frame
	Mask1 is ':247'
  [analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce]
	Changed DataFile '_MMPBSA_ligand_entropy.out' type to Evecs file for set Modes_00009
    DIAGMATRIX: Diagonalizing matrix lig.matrix and writing modes to _MMPBSA_ligand_entropy.out
	Calculating 0 eigenvectors and thermodynamic data at 298.15 K, output to STDOUT
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: 'com.top', 3907 atoms, 247 res, box: None, 2 mol, 1 frames

INPUT TRAJECTORIES:
 0: '_MMPBSA_complex.mdcrd' is an AMBER trajectory, Parm com.top (reading 1 of 1)
  Coordinate processing will occur on 1 frames.

REFERENCE FRAMES (1 total):
    0: '_MMPBSA_avgcomplex.pdb', frame 1
	Active reference frame for distance-based masks is 0
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'com.top' (6 actions):
  0: [rms mass reference :1-247]
	Target mask: [:1-247](3907)
  1: [matrix mwcovar name comp.matrix :1-247]
	Mask [:1-247] corresponds to 3907 atoms.
  2: [rms mass reference :1-246]
	Target mask: [:1-246](3817)
  3: [matrix mwcovar name rec.matrix :1-246]
	Mask [:1-246] corresponds to 3817 atoms.
  4: [rms mass reference :247]
	Target mask: [:247](90)
  5: [matrix mwcovar name lig.matrix :247]
	Mask [:247] corresponds to 90 atoms.
----- _MMPBSA_complex.mdcrd (1-1, 1) -----
100% Complete.

Read 1 frames and processed 1 frames.
TIME: Trajectory processing: 0.5628 s
TIME: Avg. throughput= 1.7769 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 3 analyses:
  0: [analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce]
Warning: In matrix 'comp.matrix', # of frames 1 is less than # of columns 11721.
Warning: The max # of non-zero eigenvalues will be 1
	Converting eigenvalues to frequencies (cm^-1), T= 298.15 K.
  1: [analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce]
Warning: In matrix 'rec.matrix', # of frames 1 is less than # of columns 11451.
Warning: The max # of non-zero eigenvalues will be 1
	Converting eigenvalues to frequencies (cm^-1), T= 298.15 K.
  2: [analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce]
Warning: In matrix 'lig.matrix', # of frames 1 is less than # of columns 270.
Warning: The max # of non-zero eigenvalues will be 1
	Converting eigenvalues to frequencies (cm^-1), T= 298.15 K.

TIME: Analyses took 0.9291 seconds.

DATASETS:
  10 data sets:
	_MMPBSA_avgcomplex.pdb:1 "_MMPBSA_avgcomplex.pdb:1" (reference), size is 1, refindex 0 (3907 atoms)
	RMSD_00001 "RMSD_00001" (double, rms), size is 1
	comp.matrix "comp.matrix" (double matrix, matrix(mass-weighted covariance)), size is 68696781
	Modes_00003 "Modes_00003" (eigenmodes(mass-weighted covariance)), size is 11721
	RMSD_00004 "RMSD_00004" (double, rms), size is 1
	rec.matrix "rec.matrix" (double matrix, matrix(mass-weighted covariance)), size is 65568426
	Modes_00006 "Modes_00006" (eigenmodes(mass-weighted covariance)), size is 11451
	RMSD_00007 "RMSD_00007" (double, rms), size is 1
	lig.matrix "lig.matrix" (double matrix, matrix(mass-weighted covariance)), size is 36585
	Modes_00009 "Modes_00009" (eigenmodes(mass-weighted covariance)), size is 270

DATAFILES:
  _MMPBSA_complex_entropy.out (Evecs file):  Modes_00003
  _MMPBSA_receptor_entropy.out (Evecs file):  Modes_00006
  _MMPBSA_ligand_entropy.out (Evecs file):  Modes_00009
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 2.0190 seconds.