--------------------------------------------------------------- Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997 --------------------------------------------------------------- 1. RESOURCE USE: | New format PARM file being parsed. | Version = 1.000 Date = 09/13/07 Time = 13:36:34 Memory Use Allocated Used Real 500000 69355 Integer 800000 131469 (static) Max Nonbonded Pairs: 668531 packed 1 to a machine word 2. DATA CONTROL: test of anal energies, compare to those from sander NTX = 1 NTXO = 0 NRC = 0 NRCX = 0 NGRPX = 70 KFORM = 1 NTB = 0 BOXX = 0.000 BOXY = 0.000 BOXZ = 0.000 BETA = 0.000 NTF = 7 NTID = 0 NTN = 0 NTNB = 0 NSNB = 0 IDIEL = 0 RCUT = 99.00 SCNB = 2.00 SCEE = 1.20 DIELC = 1.00 IMAX EBMAX EANMAX EDIHMAX ENB14MAX 1 10.00 10.00 10.00 10.00 EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX 10.00 10.00 20.00 10.00 10.00 3. A T O M I C C O O R D I N A T E S NUMBER OF ATOMS = 3238 loading the groups for analysis ----- READING GROUP 1; TITLE: first residue GRP 1 RES 50 TO 50 Number of atoms in this group = 19 ----- READING GROUP 2; TITLE: Second residue GRP 2 RES 43 TO 43 Number of atoms in this group = 22 ----- END OF GROUP READ ----- non-bonded pairs are generated in residue base and stored as residue pairs number of non-bonded residue pairs = 19900 individual pair energies greater than 10.00 kcal/mol: type groups description dist vdwnb eelnb NBOND 3- 3 O ( 85)-N2( 2940) 2.719 2.040 22.003 NBOND 3- 3 O ( 85)-H ( 2941) 1.760 0.642 -27.247 NBOND 3- 3 O ( 109)-N2( 2940) 2.734 1.858 21.765 NBOND 3- 3 HC( 116)-O ( 150) 1.795 45.189 -1.038 NBOND 3- 3 N ( 122)-C ( 149) 2.858 1.769 -28.066 NBOND 3- 3 N ( 122)-O ( 150) 2.541 5.871 28.522 NBOND 3- 3 H ( 124)-C ( 149) 2.251 -0.006 20.449 NBOND 3- 3 H ( 124)-O ( 150) 1.729 0.865 -27.840 NBOND 3- 3 O ( 126)-N2( 2940) 2.748 1.694 21.535 NBOND 3- 3 O ( 126)-N2( 2943) 2.602 4.128 24.035 NBOND 3- 3 O ( 360)-N ( 1307) 2.907 0.543 21.010 NBOND 3- 3 O ( 360)-H ( 1309) 1.937 0.077 -21.609 NBOND 3- 3 O ( 417)-oh( 3181) 2.355 12.512 20.642 NBOND 3- 3 O ( 417)-ho( 3182) 1.749 0.000 -24.072 NBOND 3- 3 OH( 418)-c3( 3184) 2.478 11.770 -2.828 NBOND 3- 3 OH( 418)-h1( 3185) 1.731 60.796 -1.454 NBOND 3- 3 CT( 438)-oh( 3181) 2.434 15.001 0.877 NBOND 3- 3 H1( 440)-oh( 3181) 1.513 314.954 -6.281 NBOND 3- 3 O ( 442)-n ( 3162) 2.884 0.655 21.004 NBOND 3- 3 H1( 446)-h1( 3159) 1.288 152.928 0.155 NBOND 3- 3 CT( 447)-hc( 3150) 1.961 27.816 -0.889 NBOND 3- 3 HC( 449)-hc( 3157) 1.595 26.474 0.423 NBOND 3- 3 HC( 450)-hc( 3150) 1.269 427.192 0.702 NBOND 3- 3 O2( 461)-N2( 1376) 2.753 1.645 30.288 NBOND 3- 3 O2( 461)-H ( 1377) 1.769 0.592 -38.080 NBOND 3- 3 O2( 462)-c3( 3136) 2.403 14.183 0.190 NBOND 3- 3 O2( 462)-h1( 3138) 1.430 494.736 -8.632 NBOND 3- 3 O2( 537)-N ( 1307) 2.859 0.796 30.578 NBOND 3- 3 O2( 537)-H ( 1308) 1.866 0.212 -32.764 NBOND 3- 3 O2( 552)-N2( 909) 2.709 2.166 31.952 NBOND 3- 3 O2( 552)-H ( 911) 1.800 0.434 -37.562 NBOND 3- 3 O2( 553)-N2( 909) 3.398 -0.184 20.316 NBOND 3- 3 O2( 553)-N2( 912) 3.110 -0.008 24.243 NBOND 3- 3 O2( 553)-H ( 914) 2.339 -0.055 -22.247 NBOND 3- 3 H ( 907)-HO( 948) 1.470 0.000 21.193 NBOND 3- 3 CA( 908)-HO( 948) 2.274 0.000 20.707 NBOND 3- 3 N2( 912)-OH( 947) 2.770 1.987 20.826 NBOND 3- 3 N2( 912)-HO( 948) 1.904 0.000 -31.551 NBOND 3- 3 H ( 913)-OH( 947) 1.886 0.294 -23.316 NBOND 3- 3 H ( 913)-HO( 948) 1.200 0.000 41.235 NBOND 3- 3 N ( 929)-O2( 963) 2.852 0.836 30.773 NBOND 3- 3 H ( 931)-O2( 963) 1.845 0.272 -33.247 NBOND 3- 3 O2( 963)-OH( 1178) 2.889 0.311 21.556 NBOND 3- 3 O ( 1181)-N ( 1390) 2.805 1.169 22.031 NBOND 3- 3 O ( 1181)-H ( 1391) 1.948 0.063 -20.855 NBOND 3- 3 N2( 1373)-O ( 1653) 2.711 2.149 22.141 NBOND 3- 3 N2( 1373)-O ( 1677) 2.709 2.176 22.174 NBOND 3- 3 H ( 1374)-O ( 1653) 1.744 0.749 -27.755 NBOND 3- 3 H ( 1375)-O ( 1677) 2.045 -0.018 -20.197 NBOND 3- 3 N2( 1376)-O ( 1694) 2.691 2.429 22.469 NBOND 3- 3 OH( 1511)-N ( 1543) 2.762 2.090 27.050 NBOND 3- 3 OH( 1511)-H ( 1544) 1.776 0.857 -29.880 NBOND 3- 3 N ( 1543)-N ( 3110) 3.144 0.182 28.372 NBOND 3- 3 N ( 1543)-H ( 3112) 2.508 -0.050 -20.355 NBOND 3- 3 HC( 1684)-O ( 1718) 1.685 98.767 -1.178 NBOND 3- 3 N ( 1690)-C ( 1717) 2.849 1.861 -28.244 NBOND 3- 3 N ( 1690)-O ( 1718) 2.527 6.357 28.836 NBOND 3- 3 H ( 1692)-C ( 1717) 2.020 0.225 25.403 NBOND 3- 3 H ( 1692)-O ( 1718) 1.634 2.029 -31.168 NBOND 3- 3 O ( 1928)-N ( 2874) 2.913 0.518 20.930 NBOND 3- 3 O ( 1928)-H ( 2876) 1.941 0.071 -21.515 NBOND 3- 3 C ( 1984)-oh( 3181) 2.867 1.169 -20.043 NBOND 3- 3 O2( 1985)-oh( 3181) 2.352 12.707 29.851 NBOND 3- 3 H1( 2007)-h1( 3186) 1.408 51.907 -0.193 NBOND 3- 3 H1( 2013)-h1( 3213) 1.413 49.728 0.160 NBOND 3- 3 CT( 2014)-hc( 3212) 2.032 17.755 -0.294 NBOND 3- 3 HC( 2016)-hc( 3207) 1.649 17.545 0.501 NBOND 3- 3 HC( 2017)-hc( 3212) 1.342 216.919 0.223 NBOND 3- 3 O2( 2028)-N2( 2943) 2.731 1.888 30.771 NBOND 3- 3 O2( 2028)-H ( 2944) 1.744 0.748 -39.166 NBOND 3- 3 O2( 2029)-h1( 3196) 1.421 535.016 -7.470 NBOND 3- 3 O2( 2104)-N ( 2874) 2.858 0.798 30.583 NBOND 3- 3 O2( 2104)-H ( 2875) 1.867 0.210 -32.734 NBOND 3- 3 O2( 2119)-N2( 2476) 2.709 2.167 31.954 NBOND 3- 3 O2( 2119)-H ( 2478) 1.801 0.433 -37.550 NBOND 3- 3 O2( 2120)-N2( 2476) 3.399 -0.184 20.306 NBOND 3- 3 O2( 2120)-N2( 2479) 3.131 -0.035 23.928 NBOND 3- 3 O2( 2120)-H ( 2481) 2.361 -0.054 -21.847 NBOND 3- 3 CT( 2354)-ha( 3236) 1.999 19.224 0.781 NBOND 3- 3 CT( 2360)-ca( 3235) 1.527 5719.639 -0.655 NBOND 3- 3 CT( 2360)-ha( 3236) 0.465 845207984.713 -4.767 NBOND 3- 3 CT( 2360)-ca( 3237) 2.440 17.938 0.818 NBOND 3- 3 HC( 2361)-ca( 3235) 1.851 50.337 0.244 NBOND 3- 3 HC( 2361)-ha( 3236) 1.117 1732.737 0.453 NBOND 3- 3 HC( 2362)-ca( 3235) 1.531 510.215 0.357 NBOND 3- 3 HC( 2362)-ha( 3236) 0.926 16454.972 0.659 NBOND 3- 3 CT( 2363)-ca( 3235) 1.429 12638.593 -1.146 NBOND 3- 3 CT( 2363)-ha( 3236) 1.474 806.690 -0.728 NBOND 3- 3 CT( 2363)-ca( 3237) 1.357 23573.048 4.057 NBOND 3- 3 CT( 2363)-ha( 3238) 1.359 2150.081 -1.547 NBOND 3- 3 HC( 2365)-cp( 3229) 1.863 46.488 0.872 NBOND 3- 3 HC( 2365)-ca( 3233) 1.982 21.557 -0.440 NBOND 3- 3 HC( 2365)-ca( 3235) 1.098 27995.472 0.547 NBOND 3- 3 HC( 2365)-ca( 3237) 0.864 497002.694 -2.821 NBOND 3- 3 HC( 2365)-ha( 3238) 1.643 15.987 0.298 NBOND 3- 3 HC( 2366)-ca( 3237) 1.439 1082.904 -1.018 NBOND 3- 3 HC( 2366)-ha( 3238) 0.634 1553537.673 2.003 NBOND 3- 3 H ( 2474)-HO( 2515) 1.457 0.000 21.570 NBOND 3- 3 CA( 2475)-HO( 2515) 2.263 0.000 20.900 NBOND 3- 3 N2( 2479)-OH( 2514) 2.763 2.080 20.939 NBOND 3- 3 N2( 2479)-HO( 2515) 1.894 0.000 -31.865 NBOND 3- 3 H ( 2480)-OH( 2514) 1.879 0.318 -23.502 NBOND 3- 3 H ( 2480)-HO( 2515) 1.191 0.000 41.881 NBOND 3- 3 N ( 2496)-O2( 2530) 2.829 0.989 31.281 NBOND 3- 3 H ( 2498)-O2( 2530) 1.829 0.320 -33.799 NBOND 3- 3 O ( 2748)-N ( 2957) 2.833 0.959 21.592 NBOND 3- 3 O ( 2748)-H ( 2958) 1.964 0.045 -20.523 NBOND 3- 3 OH( 3078)-N ( 3110) 2.725 2.614 27.793 NBOND 3- 3 OH( 3078)-H ( 3111) 1.768 0.920 -30.145 NBOND 3- 3 o ( 3142)-h1( 3159) 1.747 42.386 -0.574 NBOND 3- 3 ha( 3222)-ha( 3238) 1.381 116.361 2.148 DECOMPOSITION OF ENERGY INTO GROUPS INITIAL ENERGY COMPONENTS TOTAL ENERGY = 847348208.9494 NON-BONDED VDW ENERGY = 847352812.0684 NON-BONDED EEL ENERGY = -4603.1190 HBOND 10-12 ENERGY = 0.0000 BOND ENERGY = 0.0000 ANGLE ENERGY = 0.0000 DIHEDRAL ENERGY = 0.0000 NON-BOND 14 VDW ENERGY = 0.0000 NON-BOND 14 EEL ENERGY = 0.0000 BOND CONSTRAINT ENERGY = 0.0000 ANGLE CONSTRAINT ENERGY = 0.0000 DIHEDRAL CONSTRAINT ENERGY = 0.0000 POSITION CONSTRAINT ENERGY = 0.0000 ENERGY CONTRIBUTION BY GROUPS GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB EELNB HBOND CONSTRAINT TOTAL 1 0.00 0.00 0.00 0.00 0.00 -1.33 -16.93 0.00 0.00 -18.256 2 0.00 0.00 0.00 0.00 0.00 -7.10 -26.12 0.00 0.00 -33.226 3 0.00 0.00 0.00 0.00 0.00********** -4560.07 0.00 0.00************ TOTAL 0.00 0.00 0.00 0.00 0.00********** -4603.12 0.00 0.00************ BOND + ANGLE + DIHED INTERACTION ENERGY MATRIX 1 2 3 1 0.000 0.000 0.000 2 0.000 0.000 0.000 3 0.000 0.000 0.000 INDIVIDUAL GROUPS INTERACTION GROUP INTRA INTER TOTAL 1 0.00 0.00 0.00 2 0.00 0.00 0.00 3 0.00 0.00 0.00 TOTAL 0.00 0.00 0.00 VDW (N-B + 1-4) INTERACTION ENERGY MATRIX 1 2 3 1 2.398 -0.001 -7.450 2 -0.001 -0.508 -13.191 3 -7.450 -13.191*********** INDIVIDUAL GROUPS INTERACTION GROUP INTRA INTER TOTAL 1 2.40 -7.45 -5.05 2 -0.51 -13.19 -13.70 3*********** -20.64*********** TOTAL*********** -20.64*********** ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX 1 2 3 1 0.147 -0.004 -34.147 2 -0.004 -2.273 -47.694 3 -34.147 -47.694 -4519.148 INDIVIDUAL GROUPS INTERACTION GROUP INTRA INTER TOTAL 1 0.15 -34.15 -34.00 2 -2.27 -47.70 -49.97 3 -4519.15 -81.84 -4600.99 TOTAL -4521.27 -81.84 -4603.12 HBOND INTERACTION ENERGY MATRIX 1 2 3 1 0.000 0.000 0.000 2 0.000 0.000 0.000 3 0.000 0.000 0.000 INDIVIDUAL GROUPS INTERACTION GROUP INTRA INTER TOTAL 1 0.00 0.00 0.00 2 0.00 0.00 0.00 3 0.00 0.00 0.00 TOTAL 0.00 0.00 0.00 TOTAL INTERACTION ENERGY MATRIX 1 2 3 1 2.545 -0.004 -41.597 2 -0.004 -2.781 -60.885 3 -41.597 -60.885*********** INDIVIDUAL GROUPS INTERACTION GROUP INTRA INTER TOTAL 1 2.54 -41.60 -39.06 2 -2.78 -60.89 -63.67 3*********** -102.48*********** TOTAL*********** -102.49***********