Read in control variables Read in atom names... Read in charges... Read in masses... Read in IAC (atoms involved in L-J)... Read in NUMEX (index to excl atom list)... Read in NNO (index for nonbond of @type)... Read in residue labels... Read in the residue to atom pointer list... Read in bond parameters RK and REQ... Read in angle parameters TK and TEQ... Read in dihedral parameters PK, PN and PHASE... Read in SOLTY... Read in L-J parameters CN1 and CN2... Read in info for bonds w/ hydrogen... Read in info for bonds w/out hydrogen... Read in info for angles w/ hydrogen... Read in info for angles w/out hydrogen... Read in info for dihedrals w/ hydrogen... Read in info for dihedrals w/out hydrogen... Read in excluded atom list... Read in h-bond parameters: AG, BG, and HBCUT... Read in atomic symbols (types)... Read in tree information... Read in the JOIN info... Read in the IROTAT info... Checking coordinates: 1rrb_vac.mdcrd Amber8 Module: ptraj ASN THR ILE ARG VAL PHE LEU PRO ASN LYS GLN ARG THR VAL VAL ASN VAL ARG ASN GLY MET SER LEU HIP ASP CYS LEU MET LYS ALA LEU LYS VAL ARG GLY LEU GLN PRO GLU CYS CYS ALA VAL PHE ARG LEU LEU HID GLU HIP LYS GLY LYS LYS ALA ARG LEU ASP TRP ASN THR ASP ALA ALA SER LEU ILE GLY GLU GLU LEU GLN VAL ASP PHE LEU Successfully completed readParm. PTRAJ: Processing input file... Input is from file ptraj.in PTRAJ: trajin 1rrb_vac.mdcrd PTRAJ: matrix dist @CA out 1rrb_vac_distmat.dat Mask [@CA] represents 76 atoms PTRAJ: matrix mwcovar name 1rrb_vac_mwcovarmat out 1rrb_vac_mwcovarmat.dat Mask [*] represents 1241 atoms PTRAJ: analyze matrix 1rrb_vac_mwcovarmat out 1rrb_vac_mwcovarmat_evecs.dat vecs 5 thermo PTRAJ: matrix distcovar :1-76@CA name 1rrb_vac_distcovarmat out 1rrb_vac_distcovarmat.dat Mask [:1-76@CA] represents 76 atoms PTRAJ: analyze matrix 1rrb_vac_distcovarmat out 1rrb_vac_distcovarmat_evecs.dat vecs 5 reduce FYI: No output trajectory specified (trajout), none will be saved. PTRAJ: Successfully read the input file. Coordinate processing will occur on 10 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (1rrb_vac.mdcrd) is an AMBER trajectory with 10 sets OUTPUT COORDINATE FILE NULL entry ACTIONS 1> MATRIX: Calculating distance matrix by atom, dumping to file 1rrb_vac_distmat.dat, using no mass weighting Atom selection 1 follows :1-76@CA 7> MATRIX: Calculating mass weighted covar matrix by atom, dumping to file 1rrb_vac_mwcovarmat.dat, using no mass weighting Storing matrix on internal stack with name: 1rrb_vac_mwcovarmat Atom selection 1 follows * (All atoms are selected) 7> MATRIX: Calculating distance covar matrix by atom, dumping to file 1rrb_vac_distcovarmat.dat, using no mass weighting Storing matrix on internal stack with name: 1rrb_vac_distcovarmat Atom selection 1 follows :1-76@CA ANALYZE 1> ANALYZE MATRIX: Analyzing matrix 1rrb_vac_mwcovarmat and dumping results to 1rrb_vac_mwcovarmat_evecs.dat Calculating 5 eigenvectors and thermodynamic data 2> ANALYZE MATRIX: Analyzing matrix 1rrb_vac_distcovarmat and dumping results to 1rrb_vac_distcovarmat_evecs.dat Calculating 5 eigenvectors and no thermodynamic data Eigenvectors will be reduced Processing AMBER trajectory file 1rrb_vac.mdcrd Set 1 .......... ERROR in readAmberTrajectory(): Set #11 is corrupted ( )... ******************* - Thermochemistry - ******************* temperature 298.150 kelvin pressure 1.00000 atm molecular mass (principal isotopes) 8693.33400 amu principal moments of inertia (nuclei only) in amu-A**2: 649815.28 852341.98 971342.29 rotational symmetry number 1. Warning-- assumption of classical behavior for rotation may cause significant error rotational temperatures (kelvin) 0.00004 0.00003 0.00002 zero point vibrational energy 222.3 (joules/mol) 0.05309 (kcal/mol) 0.0000847 (hartree/particle) Warning-- 5 vibrations have low frequencies and may represent hindered internal rotations. The contributions printed below assume that these really are vibrations. freq. E Cv S cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin -------------------------------------------------------------------------------- Total 4.737 15.886 148.773 translational 0.888 2.979 52.992 rotational 0.888 2.979 52.127 vibrational 2.961 9.928 43.654 1 3.749 0.592 1.986 9.952 2 5.534 0.592 1.986 9.179 3 7.506 0.592 1.986 8.574 4 9.560 0.592 1.986 8.094 5 10.783 0.592 1.985 7.855 PTRAJ: Successfully read in 10 sets and processed 10 sets. Dumping accumulated results (if any) PTRAJ MATRIX: Dumping matrix values PTRAJ MATRIX: Dumping matrix values PTRAJ MATRIX: Dumping matrix values PTRAJ: Analyzing accumulated data