X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMD%2Fff_e0g%2F1lq7.out_GB;fp=examples%2Funres%2FMD%2Fff_e0g%2F1lq7.out_GB;h=0000000000000000000000000000000000000000;hp=11b4bada3e7327a3e8c9c812b70022fa0cadf3ff;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MD/ff_e0g/1lq7.out_GB b/examples/unres/MD/ff_e0g/1lq7.out_GB deleted file mode 100644 index 11b4bad..0000000 --- a/examples/unres/MD/ff_e0g/1lq7.out_GB +++ /dev/null @@ -1,884 +0,0 @@ --------------------------------------------------------------------------------- - FILE ASSIGNMENT --------------------------------------------------------------------------------- - Input file : 1lq7.inp - Output file : 1lq7.out_GB - - Sidechain potential file : - ../../PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc - SCp potential file : ../../PARAM/scp.parm - Electrostatic potential file : ../../PARAM/electr_631Gdp.parm - Cumulant coefficient file : ../../PARAM/fourier_opt.parm.1igd_hc_iter3_3 - Torsional parameter file : ../../PARAM/torsion_631Gdp.parm - Double torsional parameter file : ../../PARAM/torsion_double_631Gdp.parm - Bond & inertia constant file : ../../PARAM/bond.parm - Bending parameter file : ../../PARAM/thetaml.5parm - Rotamer parameter file : ../../PARAM/scgauss.parm - Threading database : ../../PARAM/patterns.cart --------------------------------------------------------------------------------- -******************************************************************************** -United-residue force field calculation - serial job. -******************************************************************************** - ### LAST MODIFIED 6/23/05 7:29PM by czarek - ++++ Compile info ++++ - Version 2.3 build 2522 - compiled Wed Feb 7 10:22:35 2007 - compiled by adam@matrix - OS name: Linux - OS release: 2.4.20-28.7smp - OS version: #1 SMP Thu Dec 18 11:18:31 EST 2003 - flags: - FC= mpif90 - OPT = -fast -pc 64 -tp p6 \ - -Minline=name:scalar2,scalar,transpose2,matvec2... - OPT1 = -C -g -fast -pc 64 -tp p6 - FFLAGS = -c ${OPT} - FFLAGS1 = -c ${OPT1} - BIN = ../bin/unres_MD_Tc-pgf90.exe - LIBS = -L../xdrf -lxdrf - CPPFLAGS = -DLINUX -DUNRES -DMP -DMPI -DPGI -DS... - ARCH = LINUX - PP = /lib/cpp -P - objectCSA = unres_CSA.o arcos.o cartprint.o cha... - ++++ End of compile info ++++ - -Potential is GB , exponents are 6 12 - -Disulfide bridge parameters: -S-S bridge energy: -5.50 -d0cm: 3.78 akcm: 15.10 -akth: 11.00 akct: 12.00 -v1ss: -1.08 v2ss: 7.61 v3ss: 13.70 -Random seed: -3059743. -3059743 - ran_num 0.9302273140895307 -RMSDBC = 3.0 -RMSDBC1 = 0.5 -RMSDBC1MAX = 1.5 -DRMS = 0.1 -RMSDBCM = 3.0 -Time limit (min): 60.0 - RESCALE_MODE 2 -Library routine used to diagonalize matrices. - -=========================== Parameters of the MD run =========================== - -The units are: -positions: angstrom, time: 48.9 fs -velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2 -energy: kcal/mol, temperature: K - - Number of time steps: 10000 - Initial time step of numerical integration: 0.10000 natural units - 4.89000 fs - Maximum acceleration threshold to scale down the time step: 4.00000 - Maximum predicted energy drift to reduce the timestep: 10.00000 - Maximum velocity threshold to reduce velocities: 20.00000 - Frequency of property output: 100 - Frequency of coordinate output: 1000 -Berendsen bath calculation - Temperature: 300.00000 - Coupling constant (tau): 1.00000 -Momenta will be reset at zero every 1000 steps - -============================== End of MD run setup ============================= - - -Energy-term weights (unscaled): - -WSCC= 1.709050 (SC-SC) -WSCP= 2.183100 (SC-p) -WELEC= 1.066840 (p-p electr) -WVDWPP= 0.270440 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 1.175360 (bending) -WSCLOC= 0.220700 (SC local) -WTOR= 2.657980 (torsional) -WTORD= 2.006460 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.427890 (multi-body 3-rd order) -WCORR4= 0.235410 (multi-body 4th order) -WCORR5= 0.000000 (multi-body 5th order) -WCORR6= 0.000000 (multi-body 6th order) -WTURN3= 1.681260 (turns, 3rd order) -WTURN4= 0.750800 (turns, 4th order) -WTURN6= 0.000000 (turns, 6th order) - -Hydrogen-bonding correlation between contact pairs of peptide groups - -Scaling factor of 1,4 SC-p interactions: 0.400 -General scaling factor of SC-p interactions: 1.000 - -Energy-term weights (scaled): - -WSCC= 1.709050 (SC-SC) -WSCP= 2.183100 (SC-p) -WELEC= 1.066840 (p-p electr) -WVDWPP= 0.270440 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 1.175360 (bending) -WSCLOC= 0.220700 (SC local) -WTOR= 2.657980 (torsional) -WTORD= 2.006460 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.427890 (multi-body 3-rd order) -WCORR4= 0.235410 (multi-body 4th order) -WCORR5= 0.000000 (multi-body 5th order) -WCORR6= 0.000000 (multi-body 6th order) -WTURN3= 1.681260 (turns, 3rd order) -WTURN4= 0.750800 (turns, 4th order) -WTURN6= 0.000000 (turns, 6th order) - Reference temperature for weights calculation: 300.0000000000000 - Parameters of the SS-bond potential: - D0CM 3.780000000000000 AKCM 15.10000000000000 AKTH - 11.00000000000000 AKCT 12.00000000000000 - V1SS -1.080000000000000 V2SS 7.610000000000000 V3SS - 13.70000000000000 - EBR -5.500000000000000 -PDB data will be read from file 1lq7.pdb - 1 10 GLY -8.202 -15.036 -3.535 - 2 12 SER -5.756 -12.694 -5.224 - 3 18 ARG -5.747 -9.983 -2.583 - 4 6 VAL -3.156 -8.094 -4.594 - 5 19 LYS -6.011 -7.405 -6.981 - 6 9 ALA -8.198 -5.679 -4.419 - 7 5 LEU -4.933 -4.076 -3.371 - 8 15 GLU -3.823 -2.772 -6.748 - 9 15 GLU -6.783 -0.461 -6.269 - 10 19 LYS -5.661 0.889 -2.915 - 11 6 VAL -2.044 1.098 -4.011 - 12 19 LYS -3.004 2.831 -7.236 - 13 9 ALA -4.915 5.197 -4.984 - 14 5 LEU -1.916 5.462 -2.690 - 15 15 GLU 0.021 6.500 -5.773 - 16 15 GLU -1.962 9.436 -7.103 - 17 19 LYS -2.668 10.626 -3.580 - 18 6 VAL 0.771 10.106 -2.088 - 19 19 LYS 2.036 11.865 -5.191 - 20 9 ALA -0.745 14.427 -5.026 - 21 5 LEU 0.489 15.375 -1.575 - 22 10 GLY 2.488 18.560 -2.002 - 23 10 GLY 5.232 16.484 -0.427 - 24 10 GLY 8.481 17.952 0.843 - 25 10 GLY 8.902 15.964 4.036 - 26 18 ARG 5.810 14.005 5.001 - 27 4 ILE 5.136 11.529 2.219 - 28 15 GLU 8.682 10.217 2.041 - 29 15 GLU 8.039 8.100 5.112 - 30 5 LEU 4.758 6.589 3.979 - 31 19 LYS 6.298 6.555 0.522 - 32 19 LYS 9.057 4.423 1.995 - 33 19 LYS 6.737 1.749 3.337 - 34 7 TRP 4.597 2.250 0.255 - 35 15 GLU 7.687 1.056 -1.577 - 36 15 GLU 8.084 -1.981 0.647 - 37 5 LEU 4.338 -2.519 0.595 - 38 19 LYS 3.766 -2.464 -3.146 - 39 19 LYS 6.675 -4.878 -3.329 - 40 19 LYS 4.708 -7.100 -0.979 - 41 4 ILE 1.506 -6.910 -2.989 - 42 15 GLU 3.681 -8.195 -5.807 - 43 15 GLU 4.922 -11.365 -4.152 - 44 5 LEU 1.423 -11.691 -2.747 - 45 10 GLY 0.909 -15.357 -3.540 - 46 10 GLY 3.203 -17.845 -1.848 - 47 10 GLY 1.644 -17.131 1.526 - 48 10 GLY -1.599 -15.646 2.793 - 49 15 GLU 0.309 -13.118 4.864 - 50 6 VAL -1.486 -10.307 3.074 - 51 19 LYS -2.537 -9.161 6.525 - 52 19 LYS 0.805 -7.395 6.335 - 53 6 VAL 0.280 -5.707 2.988 - 54 15 GLU -3.134 -4.380 3.944 - 55 15 GLU -1.979 -3.130 7.324 - 56 15 GLU 0.812 -1.550 5.314 - 57 6 VAL -1.578 0.130 2.908 - 58 19 LYS -3.463 1.283 5.981 - 59 19 LYS -0.587 3.105 7.635 - 60 5 LEU -0.837 5.201 4.493 - 61 15 GLU -4.549 5.919 4.315 - 62 15 GLU -4.418 6.878 7.974 - 63 15 GLU -1.436 9.178 7.596 - 64 4 ILE -2.377 10.304 4.107 - 65 19 LYS -5.844 11.023 5.445 - 66 19 LYS -4.093 13.130 8.056 - 67 5 LEU -1.690 14.592 5.524 - Nres: 67 - 1 10 GLY -8.202 -15.036 -3.535 -8.202 -15.036 -3.535 - 2 12 SER -5.756 -12.694 -5.224 -5.823 -12.486 -6.482 - 3 18 ARG -5.747 -9.983 -2.583 -6.547 -12.158 0.219 - 4 6 VAL -3.156 -8.094 -4.594 -2.204 -8.664 -5.544 - 5 19 LYS -6.011 -7.405 -6.981 -7.559 -7.494 -9.254 - 6 9 ALA -8.198 -5.679 -4.419 -8.597 -6.043 -3.877 - 7 5 LEU -4.933 -4.076 -3.371 -4.114 -4.625 -1.777 - 8 15 GLU -3.823 -2.772 -6.748 -4.095 -2.889 -9.387 - 9 15 GLU -6.783 -0.461 -6.269 -8.761 0.596 -6.147 - 10 19 LYS -5.661 0.889 -2.915 -6.689 0.819 -0.448 - 11 6 VAL -2.044 1.098 -4.011 -1.093 0.001 -4.169 - 12 19 LYS -3.004 2.831 -7.236 -3.873 3.113 -9.896 - 13 9 ALA -4.915 5.197 -4.984 -5.544 4.995 -4.597 - 14 5 LEU -1.916 5.462 -2.690 -2.200 4.542 -0.918 - 15 15 GLU 0.021 6.500 -5.773 1.151 6.134 -7.975 - 16 15 GLU -1.962 9.436 -7.103 -4.048 10.344 -8.580 - 17 19 LYS -2.668 10.626 -3.580 -5.346 9.989 -2.114 - 18 6 VAL 0.771 10.106 -2.088 1.497 8.913 -1.660 - 19 19 LYS 2.036 11.865 -5.191 2.026 12.098 -7.838 - 20 9 ALA -0.745 14.427 -5.026 -1.489 14.255 -4.964 - 21 5 LEU 0.489 15.375 -1.575 0.016 13.736 -0.419 - 22 10 GLY 2.488 18.560 -2.002 2.488 18.560 -2.002 - 23 10 GLY 5.232 16.484 -0.427 5.232 16.484 -0.427 - 24 10 GLY 8.481 17.952 0.843 8.481 17.952 0.843 - 25 10 GLY 8.902 15.964 4.036 8.902 15.964 4.036 - 26 18 ARG 5.810 14.005 5.001 3.498 17.056 5.852 - 27 4 ILE 5.136 11.529 2.219 4.625 12.502 0.651 - 28 15 GLU 8.682 10.217 2.041 10.801 10.233 1.365 - 29 15 GLU 8.039 8.100 5.112 6.963 7.571 7.374 - 30 5 LEU 4.758 6.589 3.979 3.411 8.054 3.243 - 31 19 LYS 6.298 6.555 0.522 6.592 7.883 -1.784 - 32 19 LYS 9.057 4.423 1.995 11.401 5.557 2.644 - 33 19 LYS 6.737 1.749 3.337 7.039 1.350 6.047 - 34 7 TRP 4.597 2.250 0.255 3.310 3.456 -2.833 - 35 15 GLU 7.687 1.056 -1.577 9.435 1.439 -3.090 - 36 15 GLU 8.084 -1.981 0.647 9.874 -1.235 2.570 - 37 5 LEU 4.338 -2.519 0.595 2.426 -1.645 0.706 - 38 19 LYS 3.766 -2.464 -3.146 4.190 -0.833 -5.529 - 39 19 LYS 6.675 -4.878 -3.329 9.726 -5.272 -3.075 - 40 19 LYS 4.708 -7.100 -0.979 5.659 -6.383 1.888 - 41 4 ILE 1.506 -6.910 -2.989 0.341 -5.401 -2.786 - 42 15 GLU 3.681 -8.195 -5.807 4.890 -7.512 -7.814 - 43 15 GLU 4.922 -11.365 -4.152 7.232 -12.325 -3.099 - 44 5 LEU 1.423 -11.691 -2.747 0.247 -10.316 -1.732 - 45 10 GLY 0.909 -15.357 -3.540 0.909 -15.357 -3.540 - 46 10 GLY 3.203 -17.845 -1.848 3.203 -17.845 -1.848 - 47 10 GLY 1.644 -17.131 1.526 1.644 -17.131 1.526 - 48 10 GLY -1.599 -15.646 2.793 -1.599 -15.646 2.793 - 49 15 GLU 0.309 -13.118 4.864 2.642 -14.123 5.951 - 50 6 VAL -1.486 -10.307 3.074 -2.419 -10.381 1.953 - 51 19 LYS -2.537 -9.161 6.525 -4.203 -11.082 7.074 - 52 19 LYS 0.805 -7.395 6.335 3.296 -8.992 7.239 - 53 6 VAL 0.280 -5.707 2.988 0.109 -6.148 1.606 - 54 15 GLU -3.134 -4.380 3.944 -5.251 -5.694 3.338 - 55 15 GLU -1.979 -3.130 7.324 -1.511 -3.840 9.882 - 56 15 GLU 0.812 -1.550 5.314 2.800 -1.875 5.720 - 57 6 VAL -1.578 0.130 2.908 -2.083 -0.512 1.697 - 58 19 LYS -3.463 1.283 5.981 -5.586 -0.123 7.438 - 59 19 LYS -0.587 3.105 7.635 1.712 3.997 7.909 - 60 5 LEU -0.837 5.201 4.493 0.374 4.674 2.787 - 61 15 GLU -4.549 5.919 4.315 -6.399 4.810 2.982 - 62 15 GLU -4.418 6.878 7.974 -5.157 5.019 9.157 - 63 15 GLU -1.436 9.178 7.596 1.229 9.527 7.571 - 64 4 ILE -2.377 10.304 4.107 -2.051 9.346 2.487 - 65 19 LYS -5.844 11.023 5.445 -8.126 10.319 7.256 - 66 19 LYS -4.093 13.130 8.056 -2.925 13.297 10.885 - 67 5 LEU -1.690 14.592 5.524 0.009 13.524 4.817 - 68 21 D 0.061 16.699 8.135 0.061 16.699 8.135 -nsup= 67 nstart_sup= 0 - ITEL - 1 10 1 - 2 12 1 - 3 18 1 - 4 6 1 - 5 19 1 - 6 9 1 - 7 5 1 - 8 15 1 - 9 15 1 - 10 19 1 - 11 6 1 - 12 19 1 - 13 9 1 - 14 5 1 - 15 15 1 - 16 15 1 - 17 19 1 - 18 6 1 - 19 19 1 - 20 9 1 - 21 5 1 - 22 10 1 - 23 10 1 - 24 10 1 - 25 10 1 - 26 18 1 - 27 4 1 - 28 15 1 - 29 15 1 - 30 5 1 - 31 19 1 - 32 19 1 - 33 19 1 - 34 7 1 - 35 15 1 - 36 15 1 - 37 5 1 - 38 19 1 - 39 19 1 - 40 19 1 - 41 4 1 - 42 15 1 - 43 15 1 - 44 5 1 - 45 10 1 - 46 10 1 - 47 10 1 - 48 10 1 - 49 15 1 - 50 6 1 - 51 19 1 - 52 19 1 - 53 6 1 - 54 15 1 - 55 15 1 - 56 15 1 - 57 6 1 - 58 19 1 - 59 19 1 - 60 5 1 - 61 15 1 - 62 15 1 - 63 15 1 - 64 4 1 - 65 19 1 - 66 19 1 - 67 5 0 - ns= 0 iss: -Boundaries in phi angle sampling: -GLY 1 -180.0 180.0 -SER 2 -180.0 180.0 -ARG 3 -180.0 180.0 -VAL 4 -180.0 180.0 -LYS 5 -180.0 180.0 -ALA 6 -180.0 180.0 -LEU 7 -180.0 180.0 -GLU 8 -180.0 180.0 -GLU 9 -180.0 180.0 -LYS 10 -180.0 180.0 -VAL 11 -180.0 180.0 -LYS 12 -180.0 180.0 -ALA 13 -180.0 180.0 -LEU 14 -180.0 180.0 -GLU 15 -180.0 180.0 -GLU 16 -180.0 180.0 -LYS 17 -180.0 180.0 -VAL 18 -180.0 180.0 -LYS 19 -180.0 180.0 -ALA 20 -180.0 180.0 -LEU 21 -180.0 180.0 -GLY 22 -180.0 180.0 -GLY 23 -180.0 180.0 -GLY 24 -180.0 180.0 -GLY 25 -180.0 180.0 -ARG 26 -180.0 180.0 -ILE 27 -180.0 180.0 -GLU 28 -180.0 180.0 -GLU 29 -180.0 180.0 -LEU 30 -180.0 180.0 -LYS 31 -180.0 180.0 -LYS 32 -180.0 180.0 -LYS 33 -180.0 180.0 -TRP 34 -180.0 180.0 -GLU 35 -180.0 180.0 -GLU 36 -180.0 180.0 -LEU 37 -180.0 180.0 -LYS 38 -180.0 180.0 -LYS 39 -180.0 180.0 -LYS 40 -180.0 180.0 -ILE 41 -180.0 180.0 -GLU 42 -180.0 180.0 -GLU 43 -180.0 180.0 -LEU 44 -180.0 180.0 -GLY 45 -180.0 180.0 -GLY 46 -180.0 180.0 -GLY 47 -180.0 180.0 -GLY 48 -180.0 180.0 -GLU 49 -180.0 180.0 -VAL 50 -180.0 180.0 -LYS 51 -180.0 180.0 -LYS 52 -180.0 180.0 -VAL 53 -180.0 180.0 -GLU 54 -180.0 180.0 -GLU 55 -180.0 180.0 -GLU 56 -180.0 180.0 -VAL 57 -180.0 180.0 -LYS 58 -180.0 180.0 -LYS 59 -180.0 180.0 -LEU 60 -180.0 180.0 -GLU 61 -180.0 180.0 -GLU 62 -180.0 180.0 -GLU 63 -180.0 180.0 -ILE 64 -180.0 180.0 -LYS 65 -180.0 180.0 -LYS 66 -180.0 180.0 -LEU 67 -180.0 180.0 -D 68 -180.0 180.0 -nsup= 67 - nsup= 67 nstart_sup= 1 nstart_seq= 1 - NZ_START= 1 NZ_END= 67 - IZ_SC= 0 - Contact order: 0.3193590869183494 - Shifting contacts: 1 1 - 1 LEU 7 VAL 4 - 2 VAL 11 LEU 7 - 3 LEU 14 LYS 10 - 4 LEU 14 VAL 11 - 5 VAL 18 LEU 14 - 6 LEU 21 VAL 18 - 7 ILE 27 VAL 18 - 8 ILE 27 LEU 21 - 9 ILE 27 GLY 23 - 10 LEU 30 VAL 18 - 11 LEU 30 ILE 27 - 12 LYS 31 VAL 18 - 13 LYS 31 ILE 27 - 14 LYS 32 GLU 28 - 15 TRP 34 VAL 11 - 16 TRP 34 LEU 14 - 17 TRP 34 VAL 18 - 18 GLU 36 LYS 33 - 19 LEU 37 VAL 11 - 20 LYS 38 VAL 11 - 21 LYS 38 TRP 34 - 22 LYS 40 LEU 37 - 23 ILE 41 VAL 4 - 24 ILE 41 LEU 7 - 25 ILE 41 VAL 11 - 26 ILE 41 LEU 37 - 27 LEU 44 VAL 4 - 28 LEU 44 ILE 41 - 29 VAL 50 ARG 3 - 30 VAL 50 LEU 44 - 31 LYS 52 GLU 49 - 32 VAL 53 LEU 7 - 33 VAL 53 LEU 37 - 34 VAL 53 LYS 40 - 35 VAL 53 ILE 41 - 36 VAL 53 LEU 44 - 37 VAL 53 VAL 50 - 38 GLU 54 LEU 7 - 39 GLU 54 VAL 50 - 40 GLU 56 LYS 33 - 41 GLU 56 LEU 37 - 42 VAL 57 LEU 7 - 43 VAL 57 LYS 10 - 44 VAL 57 VAL 11 - 45 VAL 57 LEU 14 - 46 VAL 57 LEU 37 - 47 VAL 57 VAL 53 - 48 LEU 60 LEU 14 - 49 LEU 60 VAL 18 - 50 LEU 60 LEU 30 - 51 LEU 60 VAL 57 - 52 GLU 61 LYS 10 - 53 GLU 61 LEU 14 - 54 GLU 62 LYS 58 - 55 GLU 63 LEU 30 - 56 ILE 64 LEU 14 - 57 ILE 64 LYS 17 - 58 ILE 64 VAL 18 - 59 ILE 64 LEU 21 - 60 ILE 64 LEU 30 - 61 ILE 64 LEU 60 - 62 LEU 67 LEU 21 - 63 LEU 67 ARG 26 - 64 LEU 67 ILE 27 - 65 LEU 67 LEU 30 - 66 LEU 67 GLU 63 - 67 LEU 67 ILE 64 - -Geometry of the virtual chain. - Res d Theta Phi Dsc Alpha Omega -GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 -SER 2 3.784 0.000 0.000 1.276 144.939 -94.284 -ARG 3 3.785 97.666 0.000 3.636 132.847 -136.663 -VAL 4 3.785 89.333 177.476 1.461 120.485 -67.491 -LYS 5 3.785 84.811 71.708 2.751 151.871 -7.605 -ALA 6 3.785 95.278 58.423 0.765 132.978 -83.541 -LEU 7 3.785 83.231 41.781 1.874 159.456 -117.163 -GLU 8 3.786 98.730 52.453 2.655 127.393 -42.771 -GLU 9 3.786 82.425 68.389 2.246 139.933 -10.602 -LYS 10 3.786 95.627 54.877 2.673 164.411 -81.368 -VAL 11 3.785 92.658 40.616 1.461 137.613 -78.366 -LYS 12 3.785 91.698 47.994 2.812 149.544 -30.888 -ALA 13 3.784 84.681 51.646 0.765 130.308 -80.013 -LEU 14 3.785 90.248 46.537 2.017 152.909 -147.404 -GLU 15 3.786 86.046 55.069 2.502 139.867 -30.986 -GLU 16 3.784 103.344 54.915 2.712 142.391 -46.710 -LYS 17 3.785 90.833 37.628 3.118 147.778 -92.352 -VAL 18 3.785 98.873 42.913 1.460 140.342 -74.863 -LYS 19 3.785 85.218 47.394 2.658 127.030 -40.335 -ALA 20 3.785 91.907 41.951 0.766 126.974 -76.135 -LEU 21 3.786 88.266 58.560 2.061 155.447 -157.937 -GLY 22 3.785 106.265 101.124 0.000 0.000 0.000 -GLY 23 3.784 82.782 -122.635 0.000 0.000 0.000 -GLY 24 3.785 123.323 -168.063 0.000 0.000 0.000 -GLY 25 3.785 100.070 139.318 0.000 0.000 0.000 -ARG 26 3.785 113.331 -11.596 3.921 126.029 -109.245 -ILE 27 3.785 107.256 61.845 1.915 121.565 -93.204 -GLU 28 3.785 95.422 48.830 2.224 158.348 -19.209 -GLU 29 3.785 89.803 78.416 2.560 123.110 -30.298 -LEU 30 3.786 97.334 48.356 2.122 102.856 -71.033 -LYS 31 3.785 85.659 36.445 2.678 159.703 -52.243 -LYS 32 3.785 86.916 58.012 2.683 156.818 -116.068 -LYS 33 3.786 95.112 55.594 2.756 151.563 -138.866 -TRP 34 3.785 87.957 36.487 3.556 129.060 -19.927 -GLU 35 3.785 83.732 62.879 2.344 161.223 -20.594 -GLU 36 3.785 93.115 50.005 2.731 132.834 -114.702 -LEU 37 3.785 90.124 40.742 2.105 125.264 -41.593 -LYS 38 3.785 99.270 51.927 2.919 132.849 -53.798 -LYS 39 3.785 85.547 48.115 3.086 147.472 -52.556 -LYS 40 3.785 86.846 56.607 3.105 138.553 -118.164 -ILE 41 3.785 94.614 49.064 1.917 143.243 -104.324 -GLU 42 3.785 83.812 56.085 2.440 160.828 -41.860 -GLU 43 3.785 98.465 56.994 2.714 158.179 -74.861 -LEU 44 3.785 86.063 38.858 2.074 176.659 102.329 -GLY 45 3.786 97.537 133.746 0.000 0.000 0.000 -GLY 46 3.784 117.437 63.081 0.000 0.000 0.000 -GLY 47 3.785 91.425 68.516 0.000 0.000 0.000 -GLY 48 3.785 136.496 20.218 0.000 0.000 0.000 -GLU 49 3.784 90.762 -125.179 2.763 152.424 -134.490 -VAL 50 3.785 89.897 122.644 1.460 142.703 -83.682 -LYS 51 3.785 85.720 124.240 2.601 134.737 -146.671 -LYS 52 3.785 81.391 86.531 3.094 143.151 -99.233 -VAL 53 3.785 97.470 51.282 1.461 134.249 -62.621 -GLU 54 3.786 93.331 48.720 2.564 146.346 -99.045 -GLU 55 3.784 93.790 46.265 2.696 150.633 -59.911 -GLU 56 3.785 83.606 49.391 2.055 169.300 -167.852 -VAL 57 3.785 93.281 52.240 1.460 144.237 -96.089 -LYS 58 3.785 86.192 47.933 2.934 153.109 -85.425 -LYS 59 3.785 97.066 57.243 2.481 125.481 -24.034 -LEU 60 3.785 81.584 62.431 2.157 146.082 -95.013 -GLU 61 3.785 102.055 48.277 2.536 154.995 -88.741 -GLU 62 3.785 88.204 47.695 2.324 141.973 -124.114 -GLU 63 3.785 94.858 49.253 2.688 141.300 -43.881 -ILE 64 3.785 94.414 33.242 1.910 142.265 -87.362 -LYS 65 3.785 87.615 50.150 2.997 129.513 -40.349 -LYS 66 3.785 85.747 53.802 3.065 150.194 -47.165 -LEU 67 3.785 92.709 41.921 2.128 119.269 71.699 -D 68 3.785 92.709 180.000 0.000 0.000 0.000 -MD calculation. - -******************************************************************************** - - MODECALC 12 - Calling hpb_partition - Calling chainbuild - Calling MD -====================MD calculation start==================== - Initial velocities randomly generated - Initial backbone velocities - 1.4324862923909696E-002 2.3060954008253298E-002 -6.3792993845931081E-002 - -8.2464915343916019E-002 -0.2516070235700686 4.4210010401026594E-002 - 0.2349723051592712 0.2200841538295040 4.5251610843760908E-002 - -0.2124003419082547 9.9285486849185425E-002 0.2048035611662629 - 7.7626734156010748E-002 -8.7230774321129179E-004 -0.1852910092927067 - -0.2054954346205523 -0.1736398459036022 -0.1193947039305000 - 0.1245242224603375 6.3589487597254690E-002 0.1871120037722356 - 0.1085692605935111 -0.1211347283374747 0.1589635466612328 - -4.1993868126625458E-002 0.1494245316364686 -0.1751136041361389 - 4.5499187413129132E-002 0.1391643290712960 -7.4924978376189770E-002 - -0.1007527144082593 -9.4770335703041155E-002 0.1192507570729570 - 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Calling the zero-angular momentum subroutine - vcm right after adjustment: - 3.8017267830930992E-018 3.7512350992551431E-017 3.1965691017999598E-017 - - - alpha-carbon coordinates centroid coordinates - X Y Z X Y Z -GLY( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 -SER( 2) 3.78426 0.00000 0.00000 4.43080 0.82260 0.73120 -ARG( 3) 4.28912 -3.75095 0.00000 1.17596 -4.56902 -1.69032 -VAL( 4) 8.03046 -3.20295 -0.16665 8.71726 -2.03177 -0.70567 -LYS( 5) 7.67688 -2.06100 3.42423 7.63590 -0.39832 5.61546 -ALA( 6) 6.18799 -5.30750 4.67698 5.46322 -5.52299 4.56134 -LEU( 7) 8.82268 -6.85717 2.44425 8.30071 -7.65506 0.83086 -GLU( 8) 11.85440 -5.01653 3.76993 12.78377 -2.94825 5.15151 -GLU( 9) 11.15761 -7.11075 6.84573 10.47899 -8.04696 8.77080 -LYS( 10) 11.22135 -10.44209 5.04884 9.41268 -12.36911 4.64720 -VAL( 11) 14.17775 -9.43223 2.91169 14.18390 -8.52940 1.76357 -LYS( 12) 16.06915 -8.15719 5.93202 16.86946 -6.37844 7.95788 -ALA( 13) 15.29311 -11.55269 7.41177 14.58882 -11.77210 7.61579 -LEU( 14) 16.37169 -13.22143 4.19018 14.82802 -14.01166 3.16079 -GLU( 15) 19.64210 -11.36540 4.63048 21.12868 -9.35274 4.63264 -GLU( 16) 20.77100 -12.39425 8.09289 20.64392 -12.02303 10.77656 -LYS( 17) 19.47874 -15.90707 7.53054 16.69929 -16.84643 8.58747 -VAL( 18) 20.71385 -16.42375 3.99066 20.25391 -15.92687 2.69702 -LYS( 19) 24.00505 -15.07034 5.27876 25.32372 -13.19691 6.62558 -ALA( 20) 23.71944 -17.06997 8.47954 23.10453 -17.07064 8.93579 -LEU( 21) 23.56349 -20.20890 6.36917 21.72754 -20.08478 5.44187 -GLY( 22) 27.01728 -21.75015 6.50501 27.01728 -21.75015 6.50501 -GLY( 23) 26.80315 -21.39406 2.74372 26.80315 -21.39406 2.74372 -GLY( 24) 29.24486 -23.02840 0.35816 29.24486 -23.02840 0.35816 -GLY( 25) 26.86154 -24.16153 -2.35485 26.86154 -24.16153 -2.35485 -ARG( 26) 23.21990 -23.90783 -1.35311 23.23427 -26.70438 1.39581 -ILE( 27) 22.49358 -20.25567 -0.67596 23.46555 -19.72284 0.88527 -GLU( 28) 24.05305 -18.98070 -3.88059 25.73426 -18.29546 -5.16547 -GLU( 29) 20.95661 -20.02812 -5.78878 18.92408 -21.50966 -6.26736 -LEU( 30) 18.40646 -18.47368 -3.46237 18.77058 -18.96191 -1.42967 -LYS( 31) 20.92375 -15.67995 -3.03587 22.96491 -14.74211 -1.57849 -LYS( 32) 20.73018 -15.20884 -6.78658 22.65712 -16.23130 -8.34856 -LYS( 33) 16.97677 -14.72072 -6.87198 15.71556 -16.51030 -8.54531 -TRP( 34) 17.27918 -12.86697 -3.58542 18.57215 -11.38701 -0.62121 -GLU( 35) 19.35516 -10.44211 -5.62020 21.39750 -9.38283 -6.06652 -GLU( 36) 16.73961 -10.16601 -8.34229 17.49995 -11.96145 -10.25497 -LEU( 37) 14.00858 -10.09915 -5.72280 13.26441 -10.90414 -3.92609 -LYS( 38) 15.34260 -7.32398 -3.52186 17.68958 -6.50947 -1.98989 -LYS( 39) 15.81057 -5.39441 -6.74381 17.42532 -5.07894 -9.35494 -LYS( 40) 12.11516 -5.93573 -7.36012 11.89380 -8.50464 -9.08945 -ILE( 41) 11.06021 -4.79214 -3.90928 11.15078 -6.01058 -2.43172 -GLU( 42) 12.92852 -1.63304 -4.83254 15.02804 -0.43388 -4.50309 -GLU( 43) 11.03014 -0.76567 -7.99037 11.45913 -0.76128 -10.66997 -LEU( 44) 7.93968 -1.92687 -6.13997 7.57759 -3.68108 -5.09351 -GLY( 45) 5.69258 0.97986 -7.05322 5.69258 0.97986 -7.05322 -GLY( 46) 4.88038 1.47192 -10.71568 4.88038 1.47192 -10.71568 -GLY( 47) 2.80869 -1.69482 -10.77893 2.80869 -1.69482 -10.77893 -GLY( 48) 1.06608 -3.88695 -8.23228 1.06608 -3.88695 -8.23228 -GLU( 49) 2.93953 -6.92465 -9.49038 3.34039 -6.91563 -12.22399 -VAL( 50) 4.31790 -7.50616 -6.01334 4.16953 -6.68130 -4.81745 -LYS( 51) 2.80755 -10.96500 -6.30062 0.29724 -10.29715 -6.16950 -LYS( 52) 6.14544 -11.66636 -7.94087 6.36396 -11.12483 -10.97951 -VAL( 53) 8.34461 -10.23252 -5.21413 8.57856 -8.90902 -4.64191 -GLU( 54) 6.53250 -12.10043 -2.46506 4.62177 -10.97604 -1.17678 -GLU( 55) 6.54407 -15.38490 -4.34469 5.26559 -16.84589 -6.21499 -GLU( 56) 10.22301 -14.62316 -4.80443 11.12609 -14.55747 -6.64892 -VAL( 57) 10.79177 -14.06105 -1.10526 10.60859 -12.76802 -0.45154 -LYS( 58) 8.91540 -17.30608 -0.58087 6.02291 -17.69997 -0.29064 -LYS( 59) 11.16372 -19.49178 -2.70090 13.07946 -20.07683 -4.16430 -LEU( 60) 13.70165 -18.45222 -0.09205 14.92000 -16.70965 -0.45665 -GLU( 61) 11.82615 -19.08936 3.13328 10.53872 -17.51765 4.65129 -GLU( 62) 10.87124 -22.48758 1.76750 8.71512 -22.26535 0.92859 -GLU( 63) 14.39082 -23.41720 0.73138 16.34028 -23.39571 -1.11935 -ILE( 64) 16.03667 -21.55066 3.58335 16.37728 -19.67258 3.65382 -LYS( 65) 13.64353 -23.32618 5.91738 10.92453 -24.45260 6.48320 -LYS( 66) 14.91394 -26.52060 4.33482 14.51007 -28.69022 2.20786 -LEU( 67) 18.50204 -25.31733 4.35856 19.25535 -23.95034 2.91243 -D ( 68) 19.77245 -28.51176 2.77600 19.77245 -28.51176 2.77600 - -Geometry of the virtual chain. - Res d Theta Phi Dsc Alpha Omega -GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 -SER 2 3.784 0.000 0.000 1.276 144.939 -94.284 -ARG 3 3.785 97.666 0.000 3.636 132.847 -136.663 -VAL 4 3.785 89.333 177.476 1.461 120.485 -67.491 -LYS 5 3.785 84.811 71.708 2.751 151.871 -7.605 -ALA 6 3.785 95.278 58.423 0.765 132.978 -83.541 -LEU 7 3.785 83.231 41.781 1.874 159.456 -117.163 -GLU 8 3.786 98.730 52.453 2.655 127.393 -42.771 -GLU 9 3.786 82.425 68.389 2.246 139.933 -10.602 -LYS 10 3.786 95.627 54.877 2.673 164.411 -81.368 -VAL 11 3.785 92.658 40.616 1.461 137.613 -78.366 -LYS 12 3.785 91.698 47.994 2.812 149.544 -30.888 -ALA 13 3.784 84.681 51.646 0.765 130.308 -80.013 -LEU 14 3.785 90.248 46.537 2.017 152.909 -147.404 -GLU 15 3.786 86.046 55.069 2.502 139.867 -30.986 -GLU 16 3.784 103.344 54.915 2.712 142.391 -46.710 -LYS 17 3.785 90.833 37.628 3.118 147.778 -92.352 -VAL 18 3.785 98.873 42.913 1.460 140.342 -74.863 -LYS 19 3.785 85.218 47.394 2.658 127.030 -40.335 -ALA 20 3.785 91.907 41.951 0.766 126.974 -76.135 -LEU 21 3.786 88.266 58.560 2.061 155.447 -157.937 -GLY 22 3.785 106.265 101.124 0.000 0.000 180.000 -GLY 23 3.784 82.782 -122.635 0.000 0.000 180.000 -GLY 24 3.785 123.323 -168.063 0.000 0.000 180.000 -GLY 25 3.785 100.070 139.318 0.000 0.000 180.000 -ARG 26 3.785 113.331 -11.596 3.921 126.029 -109.245 -ILE 27 3.785 107.256 61.845 1.915 121.565 -93.204 -GLU 28 3.785 95.422 48.830 2.224 158.348 -19.209 -GLU 29 3.785 89.803 78.416 2.560 123.110 -30.298 -LEU 30 3.786 97.334 48.356 2.122 102.856 -71.033 -LYS 31 3.785 85.659 36.445 2.678 159.703 -52.243 -LYS 32 3.785 86.916 58.012 2.683 156.818 -116.068 -LYS 33 3.786 95.112 55.594 2.756 151.563 -138.866 -TRP 34 3.785 87.957 36.487 3.556 129.060 -19.927 -GLU 35 3.785 83.732 62.879 2.344 161.223 -20.594 -GLU 36 3.785 93.115 50.005 2.731 132.834 -114.702 -LEU 37 3.785 90.124 40.742 2.105 125.264 -41.593 -LYS 38 3.785 99.270 51.927 2.919 132.849 -53.798 -LYS 39 3.785 85.547 48.115 3.086 147.472 -52.556 -LYS 40 3.785 86.846 56.607 3.105 138.553 -118.164 -ILE 41 3.785 94.614 49.064 1.917 143.243 -104.324 -GLU 42 3.785 83.812 56.085 2.440 160.828 -41.860 -GLU 43 3.785 98.465 56.994 2.714 158.179 -74.861 -LEU 44 3.785 86.063 38.858 2.074 176.659 102.329 -GLY 45 3.786 97.537 133.746 0.000 0.000 180.000 -GLY 46 3.784 117.437 63.081 0.000 0.000 180.000 -GLY 47 3.785 91.425 68.516 0.000 0.000 180.000 -GLY 48 3.785 136.496 20.218 0.000 0.000 180.000 -GLU 49 3.784 90.762 -125.179 2.763 152.424 -134.490 -VAL 50 3.785 89.897 122.644 1.460 142.703 -83.682 -LYS 51 3.785 85.720 124.240 2.601 134.737 -146.671 -LYS 52 3.785 81.391 86.531 3.094 143.151 -99.233 -VAL 53 3.785 97.470 51.282 1.461 134.249 -62.621 -GLU 54 3.786 93.331 48.720 2.564 146.346 -99.045 -GLU 55 3.784 93.790 46.265 2.696 150.633 -59.911 -GLU 56 3.785 83.606 49.391 2.055 169.300 -167.852 -VAL 57 3.785 93.281 52.240 1.460 144.237 -96.089 -LYS 58 3.785 86.192 47.933 2.934 153.109 -85.425 -LYS 59 3.785 97.066 57.243 2.481 125.481 -24.034 -LEU 60 3.785 81.584 62.431 2.157 146.082 -95.013 -GLU 61 3.785 102.055 48.277 2.536 154.995 -88.741 -GLU 62 3.785 88.204 47.695 2.324 141.973 -124.114 -GLU 63 3.785 94.858 49.253 2.688 141.300 -43.881 -ILE 64 3.785 94.414 33.242 1.910 142.265 -87.362 -LYS 65 3.785 87.615 50.150 2.997 129.513 -40.349 -LYS 66 3.785 85.747 53.802 3.065 150.194 -47.165 -LEU 67 3.785 92.709 41.921 2.128 119.269 71.699 -D 68 3.785 92.709 180.000 0.000 0.000 180.000 - Potential energy and its components - 4223.069527427199 1417.156941757942 245.1229503015478 - -576.8404853557735 -443.4646226713600 0.0000000000000000 - 0.0000000000000000 -28.72282448527260 123.1100688267006 - -29.22028710422527 0.0000000000000000 -77.01397934788042 - 107.3231863733070 90.31391374517578 8.996107713480077 - 0.0000000000000000 -45.58016651021919 1634.047527117884 - 0.0000000000000000 0.0000000000000000 0.0000000000000000 - 0.0000000000000000 - Initial: Kinetic energy 110.2732342277786 potential energy - 4223.069527427199 total energy 4333.342761654978 - maximum acceleration 139.9965487157773 -Momenta zeroed out, time 76.79 -Momenta zeroed out, time 176.79 -Momenta zeroed out, time 276.79 -Momenta zeroed out, time 376.79 -Momenta zeroed out, time 475.70 -Momenta zeroed out, time 575.70 -Momenta zeroed out, time 675.70 -Momenta zeroed out, time 775.70 -Momenta zeroed out, time 873.76 -Momenta zeroed out, time 973.76 - - -=================================== Timing =================================== - - MD calculations setup: 4.05000E+00 - Energy & gradient evaluation: 1.40690E+02 - Stochastic MD setup: 0.00000E+00 - Stochastic MD step setup: 0.00000E+00 - MD steps: 1.42890E+02 - - -============================ End of MD calculation =========================== - - -***** Computation time: 0 hours 2 minutes 27 seconds *****