CPPTRAJ: Trajectory Analysis. V17.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 09/10/17 10:39:27 | Available memory: 26.705 GB Reading '3qx3bispynoMg.prmtop' as Amber Topology Radius Set: modified Bondi radii (mbondi) INPUT: Reading input from '_MMPBSA_cpptrajentropy.in' [trajin _MMPBSA_complex.mdcrd] Reading '_MMPBSA_complex.mdcrd' as Amber Trajectory [reference _MMPBSA_avgcomplex.pdb] Reading '_MMPBSA_avgcomplex.pdb' as PDB Setting active reference for distance-based masks: '_MMPBSA_avgcomplex.pdb' [rms mass reference :1-1383] RMSD: (:1-1383), reference is "_MMPBSA_avgcomplex.pdb:1" (:1-1383), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [matrix mwcovar name comp.matrix :1-1383] MATRIX: Calculating mass-weighted covariance matrix, output is by atom. Matrix data set is 'comp.matrix' Start: 1 Stop: Final frame Mask1 is ':1-1383' [analyze matrix comp.matrix out _MMPBSA_complex_entropy.out thermo reduce] Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated. Warning: NOTE: 'analyze matrix' is now 'diagmatrix'. Changed DataFile '_MMPBSA_complex_entropy.out' type to Evecs file for set Modes_00004 DIAGMATRIX: Diagonalizing matrix comp.matrix and writing modes to _MMPBSA_complex_entropy.out Calculating all eigenvectors. Calculating thermodynamic data at 298.15 K, output to STDOUT Storing modes with name: Modes_00004 [rms mass reference :1-1382] RMSD: (:1-1382), reference is "_MMPBSA_avgcomplex.pdb:1" (:1-1382), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [matrix mwcovar name rec.matrix :1-1382] MATRIX: Calculating mass-weighted covariance matrix, output is by atom. Matrix data set is 'rec.matrix' Start: 1 Stop: Final frame Mask1 is ':1-1382' [analyze matrix rec.matrix out _MMPBSA_receptor_entropy.out thermo reduce] Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated. Warning: NOTE: 'analyze matrix' is now 'diagmatrix'. Changed DataFile '_MMPBSA_receptor_entropy.out' type to Evecs file for set Modes_00007 DIAGMATRIX: Diagonalizing matrix rec.matrix and writing modes to _MMPBSA_receptor_entropy.out Calculating all eigenvectors. Calculating thermodynamic data at 298.15 K, output to STDOUT Storing modes with name: Modes_00007 [rms mass reference :1383] RMSD: (:1383), reference is "_MMPBSA_avgcomplex.pdb:1" (:1383), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [matrix mwcovar name lig.matrix :1383] MATRIX: Calculating mass-weighted covariance matrix, output is by atom. Matrix data set is 'lig.matrix' Start: 1 Stop: Final frame Mask1 is ':1383' [analyze matrix lig.matrix out _MMPBSA_ligand_entropy.out thermo reduce] Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated. Warning: NOTE: 'analyze matrix' is now 'diagmatrix'. Changed DataFile '_MMPBSA_ligand_entropy.out' type to Evecs file for set Modes_00010 DIAGMATRIX: Diagonalizing matrix lig.matrix and writing modes to _MMPBSA_ligand_entropy.out Calculating all eigenvectors. Calculating thermodynamic data at 298.15 K, output to STDOUT Storing modes with name: Modes_00010 ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: 3qx3bispynoMg.prmtop, 23096 atoms, 1383 res, box: None, 7 mol INPUT TRAJECTORIES (1 total): 0: '_MMPBSA_complex.mdcrd' is an AMBER trajectory, Parm 3qx3bispynoMg.prmtop (reading 11 of 11) Coordinate processing will occur on 11 frames. REFERENCE FRAMES (1 total): 0: _MMPBSA_avgcomplex.pdb:1 Active reference frame for distance-based masks is '_MMPBSA_avgcomplex.pdb:1' BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '3qx3bispynoMg.prmtop' (6 actions): 0: [rms mass reference :1-1383] Target mask: [:1-1383](23096) Reference mask: [:1-1383](23096) 1: [matrix mwcovar name comp.matrix :1-1383] Mask [:1-1383] corresponds to 23096 atoms. 2: [rms mass reference :1-1382] Target mask: [:1-1382](22980) Reference mask: [:1-1382](22980) 3: [matrix mwcovar name rec.matrix :1-1382] Mask [:1-1382] corresponds to 22980 atoms.