------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 07/18/2006 at 09:48:21 [-O]verwriting output File Assignments: | MDIN: md5.in | MDOUT: md5.out |INPCRD: md4.rst | PARM: complex_vac.top |RESTRT: md5.rst | REFC: md4.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Dynamics for 2.5ps with constraints added linearly &cntrl imin = 0, irest = 0, ntx = 1, ntb = 2, cut = 8, ntp = 2, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0, nmropt = 1, ntt = 2, nstlim = 25, dt = 0.001, ntpr = 100, ntwx = 500, ntwr = 5000 pencut = -0.1 / &wt type='REST', istep1=1,istep2=2500,value1=0.1, value2=1.0, / &wt type='END' / LISTOUT=POUT DISANG=RST2_old -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 10.272 | New format PARM file being parsed. | Version = 1.000 Date = 05/19/06 Time = 10:27:43 NATOM = 462 NTYPES = 15 NBONH = 177 MBONA = 319 NTHETH = 413 MTHETA = 489 NPHIH = 721 MPHIA = 826 NHPARM = 0 NPARM = 0 NNB = 2599 NRES = 13 NBONA = 319 NTHETA = 489 NPHIA = 826 NUMBND = 57 NUMANG = 121 NPTRA = 50 NATYP = 38 NPHB = 0 IFBOX = 1 NMXRS = 83 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 119829 | Hollerith 2787 | Integer 114093 | Max Pairs 106491 | Max Rstack 44730 | Max Istack 2310 | Total 2167 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 100, ntrx = 1, ntwr = 5000 iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 25, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Anderson (strong collision) temperature regulation: ig = 71277, vrand = 1000 temp0 = 300.00000, tempi = 300.00000 Pressure regulation: ntp = 2 pres0 = 1.00000, comp = 44.60000, taup = 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = -0.10000, tausw = 0.10000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 21.302 Box Y = 20.545 Box Z = 26.682 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 24 NFFT2 = 20 NFFT3 = 27 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 34.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: REST 1 2500 0.100000 1.000000 0 0 RESTRAINTS: Requested file redirections: LISTOUT = POUT DISANG = RST2_old Restraints will be read from file: RST2_old Here are comments from the DISANG input file: # # 23 BEN HC 23 BEN H1 3.07 Number of restraints read = 333 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = -10.00004994 Assuming uniform neutralizing plasma -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 45662 | TOTAL SIZE OF NONBOND LIST = 45662 NSTEP = 0 TIME(PS) = 34.000 TEMP(K) = 341.42 PRESS = -1377.2 Etot = 7970.4702 EKtot = 409.1100 EPtot = 7561.3602 BOND = 133.4268 ANGLE = 344.0782 DIHED = 2300.8138 1-4 NB = 134.6823 1-4 EEL = -1011.5844 VDWAALS = -110.3683 EELEC = -1167.3012 EHBOND = 0.0000 RESTRAINT = 6937.6130 EAMBER (non-restraint) = 623.7471 EKCMT = 1.9382 VIRIAL = 349.1720 VOLUME = 11677.2043 Density = 0.5967 Ewald error estimate: 0.9464E-01 ------------------------------------------------------------------------------ NMR restraints: Bond = 6937.613 Angle = 0.000 Torsion = 0.000 =============================================================================== A V E R A G E S O V E R 25 S T E P S NSTEP = 25 TIME(PS) = 34.025 TEMP(K) = 418.29 PRESS = -1762.0 Etot = 1947.3675 EKtot = 501.2313 EPtot = 1446.1362 BOND = 127.1949 ANGLE = 340.3498 DIHED = 2301.6094 1-4 NB = 137.2707 1-4 EEL = -1018.5528 VDWAALS = -232.2048 EELEC = -1164.4501 EHBOND = 0.0000 RESTRAINT = 954.9192 EAMBER (non-restraint) = 491.2170 EKCMT = 2.4554 VIRIAL = 446.2905 VOLUME = 11666.4675 Density = 0.5973 Ewald error estimate: 0.9501E-01 ------------------------------------------------------------------------------ NMR restraints: Bond = 726.926 Angle = 0.000 Torsion = 0.000 =============================================================================== R M S F L U C T U A T I O N S NSTEP = 25 TIME(PS) = 34.025 TEMP(K) = 30.18 PRESS = 179.6 Etot = 1223.0196 EKtot = 36.1590 EPtot = 1248.3998 BOND = 6.4960 ANGLE = 27.5894 DIHED = 6.6993 1-4 NB = 5.0680 1-4 EEL = 4.7860 VDWAALS = 30.8147 EELEC = 3.5328 EHBOND = 0.0000 RESTRAINT = 1221.2863 EAMBER (non-restraint) = 27.1135 EKCMT = 0.2827 VIRIAL = 45.2877 VOLUME = 6.8709 Density = 0.0004 Ewald error estimate: 0.4356E-03 ------------------------------------------------------------------------------ NMR restraints on final step: ------------------------------------------------------------------------------ Final Restraint Analysis for coords: md5.rst Restraints, deviations, and energy contributions: pencut = -0.10 ------------------------------------------------------------------------------ First atom Last atom curr. value target deviation penalty ------------------------------------------------------------------------------ C24 BEN 13 -- C25 BEN 13: 1.488 1.800 0.312 0.210 d 0: 0 C24 BEN 13 -- *O3 BEN 13: 6.139 4.600 1.539 2.791 d 0: 0 *O3 BEN 13 -- O4' DT 8: 11.050 4.080 6.970 14.553 d 0: 0 *O3 BEN 13 -- N9 DG 9: 6.059 5.090 0.969 1.557 d 0: 0 *O3 BEN 13 -- H3' DG 9: 7.470 5.330 2.140 4.092 d 0: 0 *O3 BEN 13 -- O4' DG 9: 6.518 3.600 2.918 5.779 d 0: 0 *O3 BEN 13 -- *C4' DG 9: 7.282 4.120 3.162 6.306 d 0: 0 *O3 BEN 13 -- *C4' DG 9: 7.282 6.120 1.162 1.974 d 0: 0 H22 BEN 13 -- H1' DC 10: 3.294 4.310 0.000 0.000 d 0: 0 H22 BEN 13 -- H1' DA 11: 6.367 4.970 1.397 2.485 d 0: 0 H22 BEN 13 -- H3' DA 11: 7.516 4.610 2.906 5.751 d 0: 0 *H212 BEN 13 -- H22 BEN 13: 2.754 3.680 0.000 0.000 d 0: 0 *H212 BEN 13 -- H162 BEN 13: 6.033 3.240 2.793 5.507 d 0: 0 *H212 BEN 13 -- C18 BEN 13: 6.205 4.360 1.845 3.454 d 0: 0 *H212 BEN 13 -- C14 BEN 13: 2.818 4.210 0.000 0.000 d 0: 0 *H212 BEN 13 -- O4' DA 5: 3.669 4.970 0.000 0.000 d 0: 0 *H212 BEN 13 -- H22 BEN 13: 2.754 5.370 0.000 0.000 d 0: 0 *H212 BEN 13 -- H162 BEN 13: 6.033 4.040 1.993 3.774 d 0: 0 *H212 BEN 13 -- C18 BEN 13: 6.205 5.150 1.055 1.744 d 0: 0 *H212 BEN 13 -- C14 BEN 13: 2.818 4.770 0.000 0.000 d 0: 0 *H212 BEN 13 -- O4' DA 5: 3.669 4.800 0.000 0.000 d 0: 0 *H212 BEN 13 -- H22 BEN 13: 2.754 4.420 0.000 0.000 d 0: 0 *H212 BEN 13 -- H162 BEN 13: 6.033 3.950 2.083 3.969 d 0: 0 *H212 BEN 13 -- C18 BEN 13: 6.205 5.140 1.065 1.765 d 0: 0 *H212 BEN 13 -- H4' DA 11: 7.048 4.150 2.898 5.735 d 0: 0 H162 BEN 13 -- C18 BEN 13: 2.576 3.490 0.000 0.000 d 0: 0 H17 BEN 13 -- C18 BEN 13: 2.130 3.550 0.000 0.000 d 0: 0 H17 BEN 13 -- C2' DG 3: 10.101 3.060 7.041 14.707 d 0: 0 H17 BEN 13 -- N9 DA 5: 8.480 4.680 3.800 7.689 d 0: 0 H17 BEN 13 -- N1 DT3 6: 13.311 4.330 8.981 18.909 d 0: 0 H17 BEN 13 -- *C4' DT3 6: 10.894 3.270 7.624 15.969 d 0: 0 H17 BEN 13 -- C5 DT3 6: 12.840 4.760 8.080 16.957 d 0: 0 *H212 BEN 13 -- H22 BEN 13: 2.754 4.790 0.000 0.000 d 0: 0 *H212 BEN 13 -- H162 BEN 13: 6.033 3.340 2.693 5.290 d 0: 0 *H212 BEN 13 -- H17 BEN 13: 4.141 4.860 0.000 0.000 d 0: 0 *H212 BEN 13 -- *C4' DG 9: 10.522 3.840 6.682 13.929 d 0: 0 *H212 BEN 13 -- *H2'2 DC 10: 8.320 5.880 2.440 4.742 d 0: 0 *H212 BEN 13 -- H4' DC 10: 7.283 4.300 2.983 5.919 d 0: 0 *H212 BEN 13 -- H4' DA 11: 7.048 4.970 2.078 3.959 d 0: 0 C18 BEN 13 -- C14 BEN 13: 5.530 3.540 1.990 3.769 d 0: 0 C18 BEN 13 -- N1 DC 4: 10.173 4.540 5.633 11.657 d 0: 0 C18 BEN 13 -- O4' DC 4: 7.721 3.660 4.061 8.254 d 0: 0 C18 BEN 13 -- H1' DC 10: 9.553 3.500 6.053 12.567 d 0: 0 *O6 BEN 13 -- H22 BEN 13: 6.918 4.000 2.918 5.778 d 0: 0 *O6 BEN 13 -- *H212 BEN 13: 5.238 4.810 0.428 0.396 d 0: 0 *O6 BEN 13 -- H162 BEN 13: 2.713 4.120 0.000 0.000 d 0: 0 *O6 BEN 13 -- H17 BEN 13: 2.388 5.480 0.000 0.000 d 0: 0 *O6 BEN 13 -- C18 BEN 13: 1.167 1.800 0.633 0.828 d 0: 0 *O6 BEN 13 -- C14 BEN 13: 5.249 5.030 0.219 0.104 d 0: 0 *O6 BEN 13 -- *H5'2 DA5 1: 21.617 5.220 16.397 34.968 d 0: 0 *O6 BEN 13 -- O4' DT 8: 19.722 5.320 14.402 30.648 d 0: 0 *O6 BEN 13 -- H1' DC 10: 9.497 3.670 5.827 12.079 d 0: 0 *O6 BEN 13 -- *H2'2 DC 10: 11.267 3.880 7.387 15.457 d 0: 0 *O6 BEN 13 -- *H2'2 DC 10: 11.267 4.920 6.347 13.205 d 0: 0 *O6 BEN 13 -- H4' DC 10: 10.947 3.960 6.987 14.590 d 0: 0 C14 BEN 13 -- N1 DC 4: 7.707 4.090 3.617 7.293 d 0: 0 C14 BEN 13 -- N9 DA 5: 7.090 4.180 2.910 5.762 d 0: 0 *HN BEN 13 -- H202 BEN 13: 2.914 4.780 0.000 0.000 d 0: 0 *H29 BEN 13 -- *H5'2 DA5 1: 21.800 5.030 16.770 35.776 d 0: 0 *H29 BEN 13 -- H8 DG 3: 14.221 5.190 9.031 19.016 d 0: 0 H1' DA5 1 -- H2 DA5 1: 4.408 3.970 0.438 0.415 d 0: 0 H1' DA5 1 -- H8 DA5 1: 3.710 2.730 0.980 1.581 d 0: 0 H1' DA5 1 -- H6 DT 2: 3.461 3.820 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H1' DA5 1: 2.489 3.940 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H3' DA5 1: 2.613 3.450 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H4' DA5 1: 3.992 4.400 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- *H5'2 DA5 1: 3.382 5.090 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- *H5'2 DA5 1: 3.382 5.320 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H8 DA5 1: 2.180 3.770 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H6 DT 2: 2.400 3.870 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H1' DA5 1: 2.489 3.540 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H3' DA5 1: 2.613 3.510 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H4' DA5 1: 3.992 4.550 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- *H5'2 DA5 1: 3.382 5.200 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- *H5'2 DA5 1: 3.382 5.460 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H8 DA5 1: 2.180 4.010 0.000 0.000 d 0: 0 *H2'2 DA5 1 -- H6 DT 2: 2.400 4.050 0.000 0.000 d 0: 0 H3' DA5 1 -- H8 DA5 1: 4.035 3.970 0.065 0.009 d 0: 0 H3' DA5 1 -- H6 DT 2: 4.901 3.880 1.021 1.669 d 0: 0 H4' DA5 1 -- H8 DA5 1: 4.852 4.680 0.172 0.064 d 0: 0 *H5'2 DA5 1 -- H1' DA5 1: 4.448 4.020 0.428 0.396 d 0: 0 *H5'2 DA5 1 -- H3' DA5 1: 2.128 4.060 0.000 0.000 d 0: 0 *H5'2 DA5 1 -- H1' DT 2: 9.055 4.950 4.105 8.349 d 0: 0 *H5'2 DA5 1 -- H6 DT 2: 6.246 4.500 1.746 3.241 d 0: 0 *H5'2 DA5 1 -- H3' DA5 1: 2.128 3.180 0.000 0.000 d 0: 0 *H5'2 DA5 1 -- H8 DA5 1: 3.167 3.870 0.000 0.000 d 0: 0 N9 DA5 7 -- N7 DA5 7: 2.252 3.290 0.000 0.000 d 0: 0 *O3' DA5 7 -- N9 DA5 7: 3.696 3.480 0.216 0.101 d 0: 0 *O3' DA5 7 -- C2' DA5 7: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DA5 7 -- O4' DA5 7: 2.999 4.410 0.000 0.000 d 0: 0 *O3' DA5 7 -- *C4' DA5 7: 2.698 5.640 0.000 0.000 d 0: 0 *O3' DA5 7 -- N7 DA5 7: 5.848 3.750 2.098 4.003 d 0: 0 *O3' DA5 7 -- N9 DA5 7: 3.696 4.180 0.000 0.000 d 0: 0 *O3' DA5 7 -- C2' DA5 7: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DA5 7 -- *C4' DA5 7: 2.698 4.830 0.000 0.000 d 0: 0 *O3' DA5 7 -- N7 DA5 7: 5.848 3.290 2.558 4.999 d 0: 0 C2' DA5 7 -- N9 DA5 7: 2.483 4.240 0.000 0.000 d 0: 0 C2' DA5 7 -- N7 DA5 7: 4.571 3.540 1.031 1.692 d 0: 0 C2' DA5 7 -- C5 DT 8: 4.270 3.750 0.520 0.585 d 0: 0 O4' DA5 7 -- N9 DA5 7: 2.485 3.370 0.000 0.000 d 0: 0 O4' DA5 7 -- N7 DA5 7: 4.289 4.170 0.119 0.031 d 0: 0 *C4' DA5 7 -- N9 DA5 7: 3.668 4.460 0.000 0.000 d 0: 0 *C4' DA5 7 -- C2' DA5 7: 2.623 3.220 0.000 0.000 d 0: 0 *C4' DA5 7 -- N7 DA5 7: 5.322 3.490 1.832 3.427 d 0: 0 H1' DT 2 -- H1' DA5 1: 4.888 4.640 0.248 0.133 d 0: 0 H1' DT 2 -- H6 DT 2: 3.719 3.590 0.129 0.036 d 0: 0 H1' DT 2 -- H8 DG 3: 2.603 4.100 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H1' DT 2: 2.372 4.400 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H3' DT 2: 2.512 4.480 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H6 DT 2: 2.433 3.370 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H8 DG 3: 2.226 8.580 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H1' DT 2: 2.372 5.080 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H3' DT 2: 2.512 4.010 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H4' DT 2: 3.890 4.660 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H6 DT 2: 2.433 3.550 0.000 0.000 d 0: 0 *H2'2 DT 2 -- H8 DG 3: 2.226 4.420 0.000 0.000 d 0: 0 H3' DT 2 -- H1' DT 2: 3.723 4.400 0.000 0.000 d 0: 0 H3' DT 2 -- H6 DT 2: 4.120 3.610 0.510 0.564 d 0: 0 H4' DT 2 -- H1' DA5 1: 4.456 3.510 0.946 1.507 d 0: 0 H4' DT 2 -- H1' DT 2: 3.003 3.430 0.000 0.000 d 0: 0 H4' DT 2 -- H6 DT 2: 4.831 4.480 0.351 0.268 d 0: 0 H4' DT 2 -- H4' DG 3: 6.799 2.550 4.249 8.661 d 0: 0 H6 DT 2 -- H8 DA5 1: 4.463 4.530 0.000 0.000 d 0: 0 *H73 DT 2 -- H2 DA5 1: 7.232 4.580 2.652 5.201 d 0: 0 *H73 DT 2 -- *H2'2 DA5 1: 3.610 5.500 0.000 0.000 d 0: 0 *H73 DT 2 -- H3' DA5 1: 5.700 4.790 0.910 1.429 d 0: 0 *H73 DT 2 -- *H5'2 DA5 1: 6.488 6.000 0.488 0.515 d 0: 0 *H73 DT 2 -- H8 DA5 1: 3.862 4.020 0.000 0.000 d 0: 0 *H73 DT 2 -- *H2'2 DT 2: 4.892 6.300 0.000 0.000 d 0: 0 *H73 DT 2 -- H6 DT 2: 2.966 3.210 0.000 0.000 d 0: 0 N1 DT 8 -- C5 DT 8: 2.341 3.170 0.000 0.000 d 0: 0 *O3' DT 8 -- N1 DT 8: 3.316 3.950 0.000 0.000 d 0: 0 *O3' DT 8 -- C2' DT 8: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DT 8 -- O4' DT 8: 3.310 4.340 0.000 0.000 d 0: 0 *O3' DT 8 -- C5 DT 8: 5.242 3.150 2.092 3.988 d 0: 0 *O3' DT 8 -- *C4' DG 9: 3.887 5.720 0.000 0.000 d 0: 0 *O3' DT 8 -- N7 DG 9: 5.813 4.890 0.923 1.457 d 0: 0 *O3' DT 8 -- N1 DT 8: 3.316 3.590 0.000 0.000 d 0: 0 *O3' DT 8 -- C2' DT 8: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DT 8 -- O4' DT 8: 3.310 4.160 0.000 0.000 d 0: 0 *O3' DT 8 -- C5 DT 8: 5.242 3.330 1.912 3.599 d 0: 0 *O3' DT 8 -- *C4' DG 9: 3.887 5.470 0.000 0.000 d 0: 0 *O3' DT 8 -- N7 DG 9: 5.813 5.130 0.683 0.938 d 0: 0 C2' DT 8 -- N1 DT 8: 2.545 4.170 0.000 0.000 d 0: 0 O4' DT 8 -- N1 DT 8: 2.354 3.160 0.000 0.000 d 0: 0 O4' DT 8 -- *O3' DT 8: 3.310 3.720 0.000 0.000 d 0: 0 O4' DT 8 -- C5 DT 8: 4.099 3.280 0.819 1.233 d 0: 0 C5 DT 8 -- N7 DA5 7: 4.178 3.990 0.188 0.077 d 0: 0 *C4 DT 8 -- C25 BEN 13: 5.496 4.350 1.146 1.940 d 0: 0 *C4 DT 8 -- O9 BEN 13: 6.069 3.490 2.579 5.044 d 0: 0 *C4 DT 8 -- *O3' DA5 7: 5.468 5.460 0.008 0.000 d 0: 0 *C4 DT 8 -- *O3' DA5 7: 5.468 5.230 0.238 0.123 d 0: 0 *C4 DT 8 -- C2' DA5 7: 5.055 4.770 0.285 0.176 d 0: 0 *C4 DT 8 -- *C4' DA5 7: 5.595 6.170 0.000 0.000 d 0: 0 *C4 DT 8 -- N7 DA5 7: 4.271 3.400 0.871 1.344 d 0: 0 *C4 DT 8 -- *O3' DT 8: 6.134 6.280 0.000 0.000 d 0: 0 *C4 DT 8 -- O4' DT 8: 5.202 5.220 0.000 0.000 d 0: 0 *C4 DT 8 -- C5 DT 8: 1.691 1.800 0.109 0.026 d 0: 0 H1' DG 3 -- H8 DG 3: 3.965 4.910 0.000 0.000 d 0: 0 *O3' DG 3 -- H4' DG 3: 2.626 4.910 0.000 0.000 d 0: 0 *O3' DG 3 -- H8 DG 3: 3.951 4.120 0.000 0.000 d 0: 0 *O3' DG 3 -- C4 DC 4: 3.350 4.520 0.000 0.000 d 0: 0 *O3' DG 3 -- C5 DC 4: 2.962 4.490 0.000 0.000 d 0: 0 *O3' DG 3 -- H1' DG 3: 2.599 3.840 0.000 0.000 d 0: 0 *O3' DG 3 -- C2' DG 3: 1.222 1.800 0.578 0.709 d 0: 0 *O3' DG 3 -- H4' DG 3: 2.626 4.570 0.000 0.000 d 0: 0 *O3' DG 3 -- H8 DG 3: 3.951 3.910 0.041 0.004 d 0: 0 *O3' DG 3 -- C4 DC 4: 3.350 4.430 0.000 0.000 d 0: 0 *O3' DG 3 -- C5 DC 4: 2.962 3.120 0.000 0.000 d 0: 0 C2' DG 3 -- H8 DG 3: 2.881 3.770 0.000 0.000 d 0: 0 H4' DG 3 -- H1' DG 3: 3.607 3.790 0.000 0.000 d 0: 0 H4' DG 3 -- C2' DG 3: 3.186 3.340 0.000 0.000 d 0: 0 N9 DG 9 -- N7 DG 9: 2.245 3.640 0.000 0.000 d 0: 0 N9 DG 9 -- H1' DC 10: 6.718 4.780 1.938 3.656 d 0: 0 N9 DG 9 -- H6 DC 10: 4.657 3.440 1.217 2.093 d 0: 0 *H2'2 DG 9 -- N9 DG 9: 2.670 3.910 0.000 0.000 d 0: 0 *H2'2 DG 9 -- H3' DG 9: 2.508 3.720 0.000 0.000 d 0: 0 *H2'2 DG 9 -- O4' DG 9: 2.889 4.460 0.000 0.000 d 0: 0 *H2'2 DG 9 -- *C4' DG 9: 3.062 4.950 0.000 0.000 d 0: 0 *H2'2 DG 9 -- N7 DG 9: 4.237 3.420 0.817 1.227 d 0: 0 *H2'2 DG 9 -- H6 DC 10: 2.368 4.270 0.000 0.000 d 0: 0 *H2'2 DG 9 -- N9 DG 9: 2.670 4.250 0.000 0.000 d 0: 0 *H2'2 DG 9 -- H3' DG 9: 2.508 3.700 0.000 0.000 d 0: 0 *H2'2 DG 9 -- *C4' DG 9: 3.062 5.170 0.000 0.000 d 0: 0 *H2'2 DG 9 -- N7 DG 9: 4.237 3.310 0.927 1.465 d 0: 0 *H2'2 DG 9 -- H5 DC 10: 3.121 4.490 0.000 0.000 d 0: 0 *H2'2 DG 9 -- H6 DC 10: 2.368 5.010 0.000 0.000 d 0: 0 H3' DG 9 -- N9 DG 9: 4.393 3.990 0.403 0.351 d 0: 0 H3' DG 9 -- N7 DG 9: 6.220 3.300 2.920 5.782 d 0: 0 H3' DG 9 -- H5 DC 10: 5.070 4.520 0.550 0.649 d 0: 0 O4' DG 9 -- H4' DC 10: 7.242 2.250 4.992 10.270 d 0: 0 O4' DG 9 -- H6 DC 10: 5.379 3.380 1.999 3.788 d 0: 0 O4' DG 9 -- H3' DG 9: 3.198 2.980 0.218 0.103 d 0: 0 *C4' DG 9 -- H22 BEN 13: 9.153 3.760 5.393 11.138 d 0: 0 *C4' DG 9 -- N9 DG 9: 3.712 4.190 0.000 0.000 d 0: 0 *C4' DG 9 -- N7 DG 9: 5.326 5.290 0.036 0.003 d 0: 0 *C4' DG 9 -- H1' DC 10: 7.794 4.790 3.004 5.964 d 0: 0 *C4' DG 9 -- N1 DT 8: 6.493 4.870 1.623 2.974 d 0: 0 *C4' DG 9 -- C5 DT 8: 8.125 5.210 2.915 5.771 d 0: 0 *C4' DG 9 -- H3' DG 9: 2.385 3.840 0.000 0.000 d 0: 0 N1 DC 4 -- C5 DC 4: 2.436 4.350 0.000 0.000 d 0: 0 *O3' DC 4 -- N1 DC 4: 3.292 4.920 0.000 0.000 d 0: 0 *O3' DC 4 -- N1 DC 4: 3.292 4.240 0.000 0.000 d 0: 0 *O3' DC 4 -- C2' DC 4: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DC 4 -- C4 DC 4: 5.845 4.700 1.145 1.939 d 0: 0 *O3' DC 4 -- C5 DC 4: 5.298 3.950 1.348 2.378 d 0: 0 *O3' DC 4 -- N7 DA 5: 3.177 5.290 0.000 0.000 d 0: 0 C2' DC 4 -- N1 DC 4: 2.638 4.430 0.000 0.000 d 0: 0 C2' DC 4 -- C5 DC 4: 4.554 3.740 0.814 1.221 d 0: 0 C2' DC 4 -- C2' DA 5: 6.428 4.710 1.718 3.179 d 0: 0 C4 DC 4 -- H1' DG 3: 5.144 4.980 0.164 0.059 d 0: 0 C4 DC 4 -- H8 DG 3: 4.771 4.050 0.721 1.020 d 0: 0 C4 DC 4 -- C5 DC 4: 1.423 1.800 0.377 0.307 d 0: 0 H1' DC 10 -- H6 DC 10: 3.672 4.130 0.000 0.000 d 0: 0 H1' DC 10 -- C18 BEN 13: 9.553 4.140 5.413 11.181 d 0: 0 *H2'2 DC 10 -- H1' DC 10: 2.512 4.380 0.000 0.000 d 0: 0 *H2'2 DC 10 -- C18 BEN 13: 11.143 4.360 6.783 14.149 d 0: 0 *H2'2 DC 10 -- C14 BEN 13: 6.296 4.520 1.776 3.305 d 0: 0 *H2'2 DC 10 -- H1' DC 10: 2.512 3.760 0.000 0.000 d 0: 0 *H2'2 DC 10 -- H4' DC 10: 3.775 4.820 0.000 0.000 d 0: 0 *H2'2 DC 10 -- H5 DC 10: 4.705 3.960 0.745 1.073 d 0: 0 *H2'2 DC 10 -- H6 DC 10: 2.610 4.670 0.000 0.000 d 0: 0 *H2'2 DC 10 -- H8 DA 11: 2.552 4.850 0.000 0.000 d 0: 0 H4' DC 10 -- H22 BEN 13: 5.274 4.200 1.074 1.784 d 0: 0 H4' DC 10 -- H1' DC 10: 2.891 3.800 0.000 0.000 d 0: 0 H4' DC 10 -- H6 DC 10: 4.427 4.370 0.057 0.007 d 0: 0 H4' DC 10 -- H3' DA 11: 7.323 3.180 4.143 8.432 d 0: 0 H4' DC 10 -- H4' DA 11: 6.945 2.890 4.055 8.240 d 0: 0 H5 DC 10 -- N7 DG 9: 4.738 3.980 0.758 1.100 d 0: 0 H5 DC 10 -- H6 DC 10: 2.536 3.140 0.000 0.000 d 0: 0 H6 DC 10 -- N7 DG 9: 6.202 4.310 1.892 3.557 d 0: 0 N9 DA 5 -- N7 DA 5: 2.325 3.220 0.000 0.000 d 0: 0 N9 DA 5 -- C5 DT3 6: 4.709 3.410 1.299 2.272 d 0: 0 *O3' DA 5 -- N9 DA 5: 3.321 4.190 0.000 0.000 d 0: 0 *O3' DA 5 -- C2' DA 5: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DA 5 -- *C4' DA 5: 2.918 5.730 0.000 0.000 d 0: 0 *O3' DA 5 -- N7 DA 5: 5.285 3.090 2.195 4.213 d 0: 0 *O3' DA 5 -- C2' DT3 6: 4.852 4.560 0.292 0.185 d 0: 0 *O3' DA 5 -- C5 DT3 6: 4.031 4.050 0.000 0.000 d 0: 0 *O3' DA 5 -- N9 DA 5: 3.321 4.100 0.000 0.000 d 0: 0 *O3' DA 5 -- C2' DA 5: 1.222 1.800 0.578 0.711 d 0: 0 *O3' DA 5 -- *C4' DA 5: 2.918 5.900 0.000 0.000 d 0: 0 *O3' DA 5 -- N7 DA 5: 5.285 3.210 2.075 3.953 d 0: 0 *O3' DA 5 -- C2' DT3 6: 4.852 4.510 0.342 0.254 d 0: 0 *O3' DA 5 -- C5 DT3 6: 4.031 3.760 0.271 0.160 d 0: 0 C2' DA 5 -- C14 BEN 13: 8.153 4.620 3.533 7.109 d 0: 0 C2' DA 5 -- N9 DA 5: 2.511 3.680 0.000 0.000 d 0: 0 C2' DA 5 -- N7 DA 5: 4.316 2.900 1.416 2.526 d 0: 0 C2' DA 5 -- C5 DT3 6: 4.360 3.730 0.630 0.823 d 0: 0 O4' DA 5 -- C14 BEN 13: 5.768 3.600 2.168 4.153 d 0: 0 O4' DA 5 -- N7 DA 5: 4.172 3.670 0.502 0.546 d 0: 0 *C4' DA 5 -- C14 BEN 13: 6.667 4.730 1.937 3.653 d 0: 0 *C4' DA 5 -- C2' DA 5: 2.568 3.520 0.000 0.000 d 0: 0 *C4' DA 5 -- O4' DA 5: 1.649 1.800 0.151 0.049 d 0: 0 *C4' DA 5 -- N7 DA 5: 4.621 4.560 0.061 0.008 d 0: 0 *C4' DA 5 -- H22 BEN 13: 6.906 4.500 2.406 4.670 d 0: 0 *C4' DA 5 -- C14 BEN 13: 6.667 4.440 2.227 4.281 d 0: 0 *C4' DA 5 -- N9 DA 5: 3.491 5.400 0.000 0.000 d 0: 0 *C4' DA 5 -- C2' DA 5: 2.568 3.850 0.000 0.000 d 0: 0 *C4' DA 5 -- O4' DA 5: 1.649 1.800 0.151 0.049 d 0: 0 *C4' DA 5 -- N7 DA 5: 4.621 4.590 0.031 0.002 d 0: 0 H1' DA 11 -- H2 DA 11: 4.347 3.390 0.957 1.532 d 0: 0 H1' DA 11 -- H8 DA 11: 3.884 4.080 0.000 0.000 d 0: 0 H1' DA 11 -- H6 DT3 12: 2.924 3.720 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H1' DA 11: 2.606 3.830 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H3' DA 11: 2.337 4.030 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H4' DA 11: 3.889 4.750 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H8 DA 11: 2.390 4.150 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H6 DT3 12: 2.483 3.860 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H1' DA 11: 2.606 3.610 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H3' DA 11: 2.337 4.030 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H4' DA 11: 3.889 5.030 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H8 DA 11: 2.390 4.310 0.000 0.000 d 0: 0 *H2'2 DA 11 -- H6 DT3 12: 2.483 4.590 0.000 0.000 d 0: 0 H3' DA 11 -- H1' DA 11: 4.130 3.830 0.300 0.195 d 0: 0 H3' DA 11 -- H8 DA 11: 3.863 4.070 0.000 0.000 d 0: 0 H3' DA 11 -- H6 DT3 12: 4.996 4.020 0.976 1.573 d 0: 0 H4' DA 11 -- H1' DA 11: 3.778 3.760 0.018 0.001 d 0: 0 H4' DA 11 -- H3' DA 11: 2.699 3.060 0.000 0.000 d 0: 0 H4' DA 11 -- H1' DT3 12: 7.514 3.920 3.594 7.242 d 0: 0 H4' DA 11 -- H6 DT3 12: 5.916 3.260 2.656 5.210 d 0: 0 *H5'2 DA 11 -- H4' DA 11: 2.304 3.980 0.000 0.000 d 0: 0 *H5'2 DA 11 -- H1' DT3 12: 8.755 5.300 3.455 6.942 d 0: 0 *H5'2 DA 11 -- H6 DT3 12: 7.028 4.830 2.198 4.218 d 0: 0 N1 DT3 6 -- C5 DT3 6: 2.380 3.390 0.000 0.000 d 0: 0 *O3' DT3 6 -- N1 DT3 6: 3.285 3.430 0.000 0.000 d 0: 0 *O3' DT3 6 -- C5 DT3 6: 5.304 3.650 1.654 3.041 d 0: 0 *O3' DT3 6 -- C2' DT3 6: 1.222 1.800 0.578 0.710 d 0: 0 *O3' DT3 6 -- C5 DT3 6: 5.304 3.460 1.844 3.452 d 0: 0 C2' DT3 6 -- N9 DA 5: 6.875 3.810 3.065 6.096 d 0: 0 C2' DT3 6 -- C2' DA 5: 5.596 2.850 2.746 5.405 d 0: 0 C2' DT3 6 -- N1 DT3 6: 2.465 3.850 0.000 0.000 d 0: 0 C2' DT3 6 -- *O3' DT3 6: 1.222 1.800 0.578 0.710 d 0: 0 *C4' DT3 6 -- N9 DA 5: 6.128 4.490 1.638 3.006 d 0: 0 *C4' DT3 6 -- C2' DA 5: 4.829 5.350 0.000 0.000 d 0: 0 *C4' DT3 6 -- N1 DT3 6: 3.908 4.550 0.000 0.000 d 0: 0 *C4' DT3 6 -- C2' DT3 6: 2.577 4.100 0.000 0.000 d 0: 0 *C4' DT3 6 -- C5 DT3 6: 5.710 4.660 1.050 1.732 d 0: 0 *C4' DT3 6 -- N9 DA 5: 6.128 4.950 1.178 2.010 d 0: 0 *C4' DT3 6 -- N1 DT3 6: 3.908 3.500 0.408 0.361 d 0: 0 *C4' DT3 6 -- C2' DT3 6: 2.577 3.720 0.000 0.000 d 0: 0 *C4' DT3 6 -- C5 DT3 6: 5.710 3.640 2.070 3.941 d 0: 0 *C4' DT3 6 -- C5 DT3 6: 5.710 4.370 1.340 2.360 d 0: 0 C5 DT3 6 -- N7 DA 5: 5.276 3.350 1.926 3.630 d 0: 0 *C4 DT3 6 -- N9 DA 5: 4.035 5.010 0.000 0.000 d 0: 0 *C4 DT3 6 -- N3 DA 5: 3.822 5.000 0.000 0.000 d 0: 0 *C4 DT3 6 -- *O3' DA 5: 3.368 5.300 0.000 0.000 d 0: 0 *C4 DT3 6 -- *O3' DA 5: 3.368 5.300 0.000 0.000 d 0: 0 *C4 DT3 6 -- C2' DA 5: 3.410 4.900 0.000 0.000 d 0: 0 *C4 DT3 6 -- N7 DA 5: 4.072 3.280 0.792 1.173 d 0: 0 *C4 DT3 6 -- N1 DT3 6: 3.259 5.670 0.000 0.000 d 0: 0 *C4 DT3 6 -- *O3' DT3 6: 6.316 6.200 0.116 0.029 d 0: 0 *C4 DT3 6 -- C2' DT3 6: 5.336 5.340 0.000 0.000 d 0: 0 *C4 DT3 6 -- C5 DT3 6: 1.710 1.800 0.090 0.018 d 0: 0 H1' DT3 12 -- H6 DT3 12: 3.765 3.530 0.235 0.120 d 0: 0 *H2'2 DT3 12 -- H1' DT3 12: 2.393 3.430 0.000 0.000 d 0: 0 *H2'2 DT3 12 -- *H5'2 DT3 12: 4.851 6.040 0.000 0.000 d 0: 0 *H2'2 DT3 12 -- H6 DT3 12: 3.745 3.360 0.385 0.322 d 0: 0 H4' DT3 12 -- H1' DA 11: 4.272 4.560 0.000 0.000 d 0: 0 H4' DT3 12 -- H3' DA 11: 6.918 4.750 2.168 4.154 d 0: 0 H4' DT3 12 -- H4' DA 11: 6.321 3.350 2.971 5.893 d 0: 0 H4' DT3 12 -- H1' DT3 12: 2.930 3.000 0.000 0.000 d 0: 0 H4' DT3 12 -- H6 DT3 12: 4.276 4.150 0.126 0.034 d 0: 0 *H5'2 DT3 12 -- H1' DA 11: 3.298 4.790 0.000 0.000 d 0: 0 *H5'2 DT3 12 -- H1' DT3 12: 4.619 5.100 0.000 0.000 d 0: 0 *H5'2 DT3 12 -- H6 DT3 12: 4.070 4.890 0.000 0.000 d 0: 0 *H73 DT3 12 -- H1' DA 11: 4.427 4.370 0.057 0.007 d 0: 0 *H73 DT3 12 -- *H2'2 DA 11: 2.981 5.070 0.000 0.000 d 0: 0 *H73 DT3 12 -- *H2'2 DA 11: 2.981 5.350 0.000 0.000 d 0: 0 *H73 DT3 12 -- H3' DA 11: 5.195 4.950 0.245 0.130 d 0: 0 *H73 DT3 12 -- H8 DA 11: 3.938 4.740 0.000 0.000 d 0: 0 *H73 DT3 12 -- *H2'2 DA 11: 2.981 6.040 0.000 0.000 d 0: 0 *H73 DT3 12 -- H2 DA 11: 6.249 3.230 3.019 5.996 d 0: 0 Total distance penalty: 724.483 | RMS deviation from ideal bonds : 0.0281 | RMS deviation from ideal angles: 4.604 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.00 ( 0.38% of Total) | Build the list 0.02 (31.77% of List ) | Other 0.05 (68.23% of List ) | List time 0.07 (18.82% of Nonbo) | Short_ene time 0.16 (97.71% of Direc) | Other 0.00 ( 2.29% of Direc) | Direct Ewald time 0.16 (57.31% of Ewald) | Adjust Ewald time 0.01 ( 4.26% of Ewald) | Self Ewald time 0.00 ( 0.12% of Ewald) | Fill Bspline coeffs 0.00 ( 3.82% of Recip) | Fill charge grid 0.01 (13.39% of Recip) | Scalar sum 0.02 (23.70% of Recip) | Grad sum 0.01 (10.14% of Recip) | FFT time 0.05 (48.68% of Recip) | Other 0.00 ( 0.28% of Recip) | Recip Ewald time 0.10 (36.48% of Ewald) | Force Adjust 0.00 ( 1.28% of Ewald) | Virial junk 0.00 ( 0.19% of Ewald) | Start sycnronization 0.00 ( 0.07% of Ewald) | Other 0.00 ( 0.29% of Ewald) | Ewald time 0.28 (81.12% of Nonbo) | Other 0.00 ( 0.06% of Nonbo) | Nonbond force 0.35 (89.35% of Force) | Bond/Angle/Dihedral 0.03 ( 8.45% of Force) | Other 0.01 ( 2.20% of Force) | Force time 0.39 (95.60% of Runmd) | Shake time 0.00 ( 0.34% of Runmd) | Verlet update time 0.01 ( 1.86% of Runmd) | Ekcmr time 0.00 ( 0.13% of Runmd) | Other 0.01 ( 2.07% of Runmd) | Runmd Time 0.41 (67.67% of Total) | Other 0.19 (31.94% of Total) | Total time 0.61 (99.33% of ALL ) | Highest rstack allocated: 44344 | Highest istack allocated: 462 | Job began at 09:48:21.266 on 07/18/2006 | Setup done at 09:48:21.467 on 07/18/2006 | Run done at 09:48:21.878 on 07/18/2006 | wallclock() was called 1074 times