X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMINIM%2Foutputs%2F1L2Y_min-rand.out_GB;fp=examples%2Funres%2FMINIM%2Foutputs%2F1L2Y_min-rand.out_GB;h=03c11b458b956a5a26d1c90b9245ccbb1862bfc3;hp=0000000000000000000000000000000000000000;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MINIM/outputs/1L2Y_min-rand.out_GB b/examples/unres/MINIM/outputs/1L2Y_min-rand.out_GB new file mode 100644 index 0000000..03c11b4 --- /dev/null +++ b/examples/unres/MINIM/outputs/1L2Y_min-rand.out_GB @@ -0,0 +1,296 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1L2Y_min-rand.inp + Output file : 1L2Y_min-rand.out_GB + + Sidechain potential file : + /users/adam/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k + SCp potential file : /users/adam/unres/PARAM/scp.parm + Electrostatic potential file : /users/adam/unres/PARAM/electr_631Gdp.parm + Cumulant coefficient file : + /users/adam/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : /users/adam/unres/PARAM/torsion_631Gdp.parm + Double torsional parameter file : + /users/adam/unres/PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : /users/adam/unres/PARAM/rotcorr_AM1.parm + Bond & inertia constant file : /users/adam/unres/PARAM/bond.parm + Bending parameter file : /users/adam/unres/PARAM/thetaml.5parm + Rotamer parameter file : /users/adam/unres/PARAM/scgauss.parm + Threading database : /users/adam/unres/PARAM/patterns.cart +-------------------------------------------------------------------------------- +******************************************************************************** +United-residue force field calculation - serial job. +******************************************************************************** + ### LAST MODIFIED 11/03/09 1:19PM by czarek + ++++ Compile info ++++ + Version MINI energy and minimization only + +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 +RMSDBC = 3.0 +RMSDBC1 = 0.5 +RMSDBC1MAX = 1.5 +DRMS = 0.1 +RMSDBCM = 3.0 +Time limit (min): 960.0 + RESCALE_MODE 2 +Library routine used to diagonalize matrices. + +******************************************************************************** + Options in energy minimization: +******************************************************************************** +MaxMin: 2000 MaxFun: 5000MinMin: 2000 MinFun: 2000 TolF: 1.00000E-02 RTolF: 1.00000E-04 + +Energy-term weights (unscaled): + +WSCC= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlation) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (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= 1.352790 (SC-SC) +WSCP= 1.593040 (SC-p) +WELEC= 0.715340 (p-p electr) +WVDWPP= 0.113710 (p-p VDW) +WBOND= 1.000000 (stretching) +WANG= 1.138730 (bending) +WSCLOC= 0.162580 (SC local) +WTOR= 1.985990 (torsional) +WTORD= 1.570690 (double torsional) +WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) +WEL_LOC= 0.160360 (multi-body 3-rd order) +WCORR4= 0.428870 (multi-body 4th order) +WCORR5= 0.000000 (multi-body 5th order) +WCORR6= 0.000000 (multi-body 6th order) +WSCCOR= 0.000000 (back-scloc correlatkion) +WTURN3= 1.687220 (turns, 3rd order) +WTURN4= 0.662300 (turns, 4th order) +WTURN6= 0.000000 (turns, 6th order) + Reference temperature for weights calculation: 300.000000000000 + Parameters of the SS-bond potential: + D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH + 11.0000000000000 AKCT 12.0000000000000 + V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS + 13.7000000000000 + EBR -5.50000000000000 +PDB data will be read from file 1L2Y.pdb + Nres: 21 +Backbone and SC coordinates as read from the PDB + 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051 + 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437 + 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850 + 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 + 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074 + 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853 + 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 + 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799 + 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146 + 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676 + 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593 + 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723 + 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058 + 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675 + 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546 + 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870 + 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986 + 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688 + 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856 + 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430 + 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488 + 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754 +nsup= 20 nstart_sup= 2 + ITEL + 1 21 0 + 2 14 1 + 3 5 1 + 4 8 1 + 5 4 1 + 6 13 1 + 7 7 1 + 8 5 1 + 9 19 1 + 10 16 1 + 11 10 1 + 12 10 2 + 13 20 1 + 14 12 1 + 15 12 1 + 16 10 1 + 17 18 2 + 18 20 2 + 19 20 2 + 20 20 1 + 21 12 0 + ns= 0 iss: +Boundaries in phi angle sampling: +D 1 -180.0 180.0 +ASN 2 -180.0 180.0 +LEU 3 -180.0 180.0 +TYR 4 -180.0 180.0 +ILE 5 -180.0 180.0 +GLN 6 -180.0 180.0 +TRP 7 -180.0 180.0 +LEU 8 -180.0 180.0 +LYS 9 -180.0 180.0 +ASP 10 -180.0 180.0 +GLY 11 -180.0 180.0 +GLY 12 -180.0 180.0 +PRO 13 -180.0 180.0 +SER 14 -180.0 180.0 +SER 15 -180.0 180.0 +GLY 16 -180.0 180.0 +ARG 17 -180.0 180.0 +PRO 18 -180.0 180.0 +PRO 19 -180.0 180.0 +PRO 20 -180.0 180.0 +SER 21 -180.0 180.0 +D 22 -180.0 180.0 +nsup= 20 + nsup= 20 nstart_sup= 2 nstart_seq= 2 + NZ_START= 2 NZ_END= 21 + IZ_SC= 0 + Contact order: 0.000000000000000E+000 + Shifting contacts: 2 2 +Random-generated initial geometry. + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 94.624 -178.093 +LEU 3 3.800 92.239 0.000 1.939 102.878 -79.236 +TYR 4 3.800 92.239 -180.000 2.484 163.195 -7.440 +ILE 5 3.800 90.357 45.849 1.776 144.011 -104.516 +GLN 6 3.800 89.090 55.194 2.240 170.986 -139.318 +TRP 7 3.800 88.657 49.396 2.605 123.650 -21.913 +LEU 8 3.800 93.032 48.298 1.939 151.723 -105.899 +LYS 9 3.800 94.826 46.843 2.541 106.974 -55.960 +ASP 10 3.800 87.966 59.623 1.709 153.447 -128.646 +GLY 11 3.800 89.908 56.679 0.000 0.000 0.000 +GLY 12 3.800 100.181 -87.304 0.000 0.000 0.000 +PRO 13 3.800 109.073 -127.499 1.345 101.771 -115.580 +SER 14 3.800 89.537 4.261 1.150 144.515 -129.218 +SER 15 3.800 91.815 66.108 1.150 161.047 -100.177 +GLY 16 3.800 101.784 70.140 0.000 0.000 0.000 +ARG 17 3.800 92.201 -108.949 3.020 139.846 -132.716 +PRO 18 3.800 133.225 103.824 1.345 115.610 -118.024 +PRO 19 3.800 121.502 -122.527 1.345 118.575 -122.417 +PRO 20 3.800 117.950 -90.285 1.345 118.959 -126.207 +SER 21 3.800 114.201 -108.328 1.150 128.925 -37.341 +D 22 3.800 114.201 180.000 0.000 0.000 0.000 +Energy evaluation or minimization calculation. + +Conformations will be energy-minimized. +******************************************************************************** + + Time for energy evaluation 0.000000000000000E+000 + +Virtual-chain energies: + +EVDW= -2.897067E+01 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 5.054652E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -1.018887E+02 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= -2.665276E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 3.636156E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -3.261471E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 5.789477E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 1.479510E+01 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 1.006444E+00 WEIGHT= 1.570690D+00 (double torsional) +EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -7.263447E+01 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= -4.196810E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.924843E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= 7.171768E-01 WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= -3.021986E+01 (total) + +SUMSL return code: 4 energy -79.51931 + + +Virtual-chain energies: + +EVDW= -5.120726E+01 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 4.630730E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -9.334462E+01 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= -2.041364E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 3.636156E-27 WEIGHT= 1.000000D+00 (stretching) +EBE= -3.685480E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 4.338842E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 1.030614E+01 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 3.510843E-01 WEIGHT= 1.570690D+00 (double torsional) +EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -6.845424E+01 WEIGHT= 4.288700D-01 (multi-body) +ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body) +EELLO= -5.185692E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.856072E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= -3.252103E+00 WEIGHT= 6.623000D-01 (turns, 4th order) +ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order) +ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr) +EDIHC= 0.000000E+00 (dihedral angle constraints) +ESS= 0.000000E+00 (disulfide-bridge intrinsic energy) +UCONST= 0.000000E+00 (Constraint energy) +ETOT= -7.951931E+01 (total) + +Geometry of the virtual chain. + Res d Theta Gamma Dsc Alpha Beta +D 1 0.000 0.000 0.000 0.000 0.000 0.000 +ASN 2 3.800 0.000 0.000 1.684 145.636 -16.341 +LEU 3 3.800 115.891 0.000 1.939 137.106 -20.479 +TYR 4 3.800 91.470 164.571 2.484 172.221 20.304 +ILE 5 3.800 91.922 85.116 1.776 143.240 -90.802 +GLN 6 3.800 90.239 44.027 2.240 114.569 -126.866 +TRP 7 3.800 89.768 44.854 2.605 125.459 -26.243 +LEU 8 3.800 89.846 45.610 1.939 153.751 -173.458 +LYS 9 3.800 90.114 64.235 2.541 83.102 -75.669 +ASP 10 3.800 91.773 38.260 1.709 135.700 -110.240 +GLY 11 3.800 92.683 65.542 0.000 180.000 180.000 +GLY 12 3.800 109.008 -65.773 0.000 180.000 180.000 +PRO 13 3.800 149.210 -162.848 1.345 128.883 -155.795 +SER 14 3.800 91.775 -38.027 1.150 133.697 -101.096 +SER 15 3.800 91.305 50.569 1.150 117.134 -81.693 +GLY 16 3.800 123.414 71.938 0.000 180.000 180.000 +ARG 17 3.800 97.656 -79.129 3.020 126.102 -91.006 +PRO 18 3.800 134.525 87.337 1.345 121.053 -126.854 +PRO 19 3.800 122.674 -109.034 1.345 109.296 -110.132 +PRO 20 3.800 117.844 -106.682 1.345 118.782 -122.215 +SER 21 3.800 118.382 -134.825 1.150 146.519 -119.631 +D 22 3.800 120.888 -118.739 0.000 180.000 180.000 +SUMSL return code: 4 +# of energy evaluations: 520 +# of energy evaluations/sec: 3460.000 + + +***** Computation time: 0 hours 0 minutes 0 seconds *****