Amber8 Module: ptraj L01 Successfully completed readParm. PTRAJ: Processing input file... Input is from standard input PTRAJ: trajin inhibitor.dcd PTRAJ: matrix mwcovar name mwcvmat Mask [*] represents 23 atoms PTRAJ: analyze matrix mwcvmat thermo reduce FYI: No output trajectory specified (trajout), none will be saved. PTRAJ: Successfully read the input file. Coordinate processing will occur on 2001 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (inhibitor.dcd) is a CHARMM trajectory in big endian binary format with box information representing 2001 sets NFILE = 2001 ISTEP = 0 NINTV = 1 NSAVC = 2001 NSAVV = 0 NDEGF = 0 NFREA = 0 DELTA = 1.0000 QCRYS = 1 QDIM4 = 0 VERNU = 24 NATREC= 23 NFREAT = 23 Dumping the title: Created by DCD pluginREMARKS Created 05 October, 2007 at 12:51 OUTPUT COORDINATE FILE NULL entry ACTIONS 1> MATRIX: Calculating mass weighted covar matrix by atom using no mass weighting Storing matrix on internal stack with name: mwcvmat Atom selection 1 follows * (All atoms are selected) ANALYZE 1> ANALYZE MATRIX: Analyzing matrix mwcvmat and dumping results to stdout Calculating 0 eigenvectors and thermodynamic data Processing CHARMM trajectory file inhibitor.dcd Set 1 ................................................. Set 50 ................................................. Set 100 ................................................. Set 150 ................................................. Set 200 ................................................. Set 250 ................................................. Set 300 ................................................. Set 350 ................................................. Set 400 ................................................. Set 450 ................................................. Set 500 ................................................. Set 550 ................................................. Set 600 ................................................. Set 650 ................................................. Set 700 ................................................. Set 750 ................................................. Set 800 ................................................. Set 850 ................................................. Set 900 ................................................. Set 950 ................................................. Set 1000 ................................................. Set 1050 ................................................. Set 1100 ................................................. Set 1150 ................................................. Set 1200 ................................................. Set 1250 ................................................. Set 1300 ................................................. Set 1350 ................................................. Set 1400 ................................................. Set 1450 ................................................. Set 1500 ................................................. Set 1550 ................................................. Set 1600 ................................................. Set 1650 ................................................. Set 1700 ................................................. Set 1750 ................................................. Set 1800 ................................................. Set 1850 ................................................. Set 1900 ................................................. Set 1950 ................................................. Set 2000 . ******************* - Thermochemistry - ******************* temperature 298.150 kelvin pressure 1.00000 atm molecular mass (principal isotopes) 476.77600 amu principal moments of inertia (nuclei only) in amu-A**2: 2298.75 2809.58 5091.24 rotational symmetry number 1. Warning-- assumption of classical behavior for rotation may cause significant error rotational temperatures (kelvin) 0.01055 0.00863 0.00476 zero point vibrational energy 280477.9 (joules/mol) 66.99195 (kcal/mol) 0.1068263 (hartree/particle) Warning-- 37 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 83.750 81.977 198.624 translational 0.888 2.979 44.344 rotational 0.888 2.979 35.634 vibrational 81.973 76.019 118.646 1 12.398 0.592 1.985 7.578 2 13.176 0.592 1.985 7.457 3 14.852 0.592 1.985 7.219 4 27.435 0.593 1.983 6.001 5 31.879 0.593 1.982 5.704 6 37.398 0.594 1.980 5.387 7 44.484 0.594 1.978 5.044 8 56.425 0.596 1.974 4.574 9 58.755 0.596 1.973 4.494 10 65.146 0.597 1.970 4.291 11 66.953 0.597 1.969 4.237 12 67.891 0.597 1.968 4.209 13 68.568 0.597 1.968 4.190 14 94.503 0.602 1.952 3.561 15 102.099 0.604 1.946 3.410 16 126.639 0.610 1.925 2.993 17 129.649 0.611 1.922 2.948 18 134.688 0.613 1.917 2.875 19 138.875 0.614 1.913 2.816 20 155.081 0.620 1.896 2.606 21 166.671 0.624 1.882 2.470 22 194.060 0.635 1.847 2.186 23 217.261 0.645 1.813 1.979 24 226.627 0.650 1.799 1.903 25 232.842 0.653 1.789 1.854 26 240.555 0.657 1.777 1.796 27 251.952 0.663 1.758 1.714 28 257.312 0.666 1.749 1.678 29 331.957 0.714 1.610 1.249 30 341.394 0.720 1.591 1.204 31 367.631 0.740 1.537 1.088 32 370.526 0.742 1.531 1.076 33 400.809 0.766 1.467 0.958 34 410.912 0.775 1.445 0.922 35 431.925 0.793 1.399 0.851 36 477.825 0.834 1.298 0.715 37 565.769 0.921 1.104 0.511 38 644.475 1.007 0.938 0.378 39 668.667 1.035 0.889 0.345 40 674.156 1.041 0.878 0.337 41 719.584 1.094 0.791 0.283 42 740.369 1.119 0.752 0.261 43 789.566 1.180 0.667 0.215 44 807.758 1.202 0.637 0.200 45 828.147 1.228 0.604 0.185 46 925.010 1.353 0.466 0.126 47 957.243 1.396 0.425 0.111 48 1023.458 1.484 0.351 0.085 49 1041.997 1.509 0.332 0.079 50 1131.714 1.632 0.253 0.055 51 1275.655 1.831 0.160 0.030 52 1299.873 1.865 0.148 0.027 53 1343.934 1.927 0.127 0.023 54 1380.806 1.979 0.112 0.019 55 1414.340 2.026 0.100 0.017 56 1422.929 2.039 0.097 0.016 57 1446.641 2.072 0.090 0.015 58 1454.690 2.083 0.087 0.014 59 1506.665 2.157 0.073 0.011 60 1515.781 2.170 0.071 0.011 61 1538.116 2.202 0.065 0.010 62 1549.621 2.218 0.063 0.009 63 1587.861 2.272 0.055 0.008 64 1598.848 2.288 0.053 0.008 65 1635.587 2.340 0.046 0.007 66 1670.135 2.389 0.041 0.006 67 1741.731 2.491 0.031 0.004 68 1758.847 2.516 0.029 0.004 69 1831.554 2.619 0.022 0.003 PTRAJ: Successfully read in 2002 sets and processed 2001 sets. Dumping accumulated results (if any) PTRAJ: Analyzing accumulated data