Amber8 Module: ptraj L01 Successfully completed readParm. PTRAJ: Processing input file... Input is from standard input PTRAJ: trajin inhibitor.dcd PTRAJ: rms first * Mask [*] represents 23 atoms 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> RMS to first frame using no mass weighting Atom selection follows * (All atoms are selected) 7> 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: 2298.63 2831.90 5113.42 rotational symmetry number 1. Warning-- assumption of classical behavior for rotation may cause significant error rotational temperatures (kelvin) 0.01055 0.00857 0.00474 zero point vibrational energy 1134633677.8 (joules/mol) 271006.48185 (kcal/mol) 432.1506473 (hartree/particle) Warning-- 33 vibrations have low frequencies and may represent hindered internal rotations. The contributions printed below assume that these really are vibrations. warning: setting vibrational entropy to zero for mode 68 with vtemp = -26264214.2644639 warning: setting vibrational entropy to zero for mode 69 with vtemp = -8664197.38173059 freq. E Cv S cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin -------------------------------------------------------------------------------- Total 340383.423 NaN 164.885 translational 0.888 2.979 44.344 rotational 0.888 2.979 35.646 vibrational 340381.646 NaN 84.895 1 15.907 0.592 1.985 7.083 2 36.371 0.594 1.981 5.442 3 48.070 0.595 1.977 4.891 4 50.137 0.595 1.976 4.807 5 56.973 0.596 1.973 4.555 6 64.591 0.597 1.970 4.307 7 66.675 0.597 1.969 4.245 8 67.909 0.597 1.968 4.209 9 76.204 0.599 1.964 3.982 10 103.566 0.604 1.945 3.382 11 121.014 0.609 1.930 3.081 12 123.078 0.609 1.928 3.048 13 126.879 0.610 1.925 2.989 14 157.156 0.620 1.893 2.581 15 161.011 0.622 1.889 2.535 16 178.765 0.628 1.867 2.338 17 202.322 0.638 1.835 2.109 18 216.958 0.645 1.814 1.982 19 222.629 0.648 1.805 1.935 20 265.321 0.671 1.735 1.624 21 277.377 0.678 1.714 1.548 22 302.829 0.694 1.667 1.399 23 313.473 0.701 1.646 1.342 24 372.596 0.744 1.527 1.067 25 403.232 0.768 1.462 0.949 26 406.427 0.771 1.455 0.938 27 421.958 0.784 1.421 0.884 28 434.369 0.795 1.394 0.843 29 468.711 0.826 1.318 0.740 30 495.144 0.851 1.259 0.669 31 620.624 0.981 0.987 0.415 32 647.926 1.011 0.931 0.373 33 667.897 1.034 0.890 0.346 34 681.455 1.050 0.864 0.328 35 721.374 1.097 0.787 0.281 36 734.508 1.112 0.763 0.267 37 784.077 1.173 0.676 0.220 38 800.684 1.194 0.648 0.206 39 827.844 1.228 0.605 0.185 40 967.199 1.409 0.413 0.106 41 990.147 1.440 0.387 0.097 42 1010.086 1.466 0.365 0.089 43 1050.496 1.521 0.324 0.076 44 1083.776 1.566 0.293 0.066 45 1188.888 1.711 0.212 0.043 46 1197.236 1.722 0.206 0.042 47 1252.219 1.799 0.173 0.033 48 1276.487 1.833 0.159 0.030 49 1291.974 1.854 0.151 0.028 50 1307.132 1.876 0.144 0.026 51 1350.210 1.936 0.125 0.022 52 1393.429 1.997 0.108 0.018 53 1417.499 2.031 0.099 0.017 54 1444.700 2.069 0.090 0.015 55 1466.394 2.100 0.084 0.013 56 1568.481 2.245 0.059 0.009 57 1583.474 2.266 0.056 0.008 58 1603.147 2.294 0.052 0.008 59 1648.998 2.359 0.044 0.006 60 1677.489 2.400 0.040 0.005 61 1706.853 2.442 0.036 0.005 62 1757.281 2.513 0.030 0.004 63 1810.534 2.589 0.024 0.003 64********** 6657.325 NaN 0.000 65********** 26253.291 NaN 0.000 66********** 61634.738 NaN 0.000 67********** 211077.383 NaN 0.000 68********** 26078.713 0.000 0.000 69********** 8603.003 0.000 0.000 PTRAJ: Successfully read in 2002 sets and processed 2001 sets. Dumping accumulated results (if any) PTRAJ: Analyzing accumulated data