-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : small.inp Output file : small.out_GB000 Sidechain potential file : /users/czarek/UNRES/GIT/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16- 10-8k SCp potential file : /users/czarek/UNRES/GIT/unres/PARAM/scp.parm Electrostatic potential file : /users/czarek/UNRES/GIT/unres/PARAM/electr_631Gdp.parm Cumulant coefficient file : /users/czarek/UNRES/GIT/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 Torsional parameter file : /users/czarek/UNRES/GIT/unres/PARAM/torsion_631Gdp.parm Double torsional parameter file : /users/czarek/UNRES/GIT/unres/PARAM/torsion_double_631Gdp.parm SCCOR parameter file : /users/czarek/UNRES/GIT/unres/PARAM/sccor_pdb_shelly.dat Bond & inertia constant file : /users/czarek/UNRES/GIT/unres/PARAM/bond.parm Bending parameter file : /users/czarek/UNRES/GIT/unres/PARAM/thetaml.5parm Rotamer parameter file : /users/czarek/UNRES/GIT/unres/PARAM/scgauss.parm Threading database : /users/czarek/UNRES/GIT/unres/PARAM/patterns.cart -------------------------------------------------------------------------------- ******************************************************************************** United-residue force field calculation - parallel job. ******************************************************************************** ### LAST MODIFIED 03/28/12 23:29 by czarek ++++ Compile info ++++ Version 3.1 build 41 compiled Fri Feb 15 01:43:03 2013 compiled by czarek@piasek3 OS name: Linux OS release: 2.6.32-42-generic OS version: #96-Ubuntu SMP Wed Aug 15 19:37:37 UTC 2012 flags: INSTALL_DIR = /users/software/mpich-1.2.7p1_int... FC= ifort OPT = -O3 -ip -w FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)... FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ... LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr... ARCH = LINUX PP = /lib/cpp -P object = unres.o arcos.o cartprint.o chainbuild... GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ... GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP... E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR... E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort... ++++ 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 MPI: node= 0 iseed(4)= 0 0 -16 -62756 ran_num 6.422640197456531E-013 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= 1.000000 (SC-SC) WSCP= 2.794050 (SC-p) WELEC= 0.145810 (p-p electr) WVDWPP= 0.145810 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.956840 (bending) WSCLOC= 0.170100 (SC local) WTOR= 2.046980 (torsional) WTORD= 1.696240 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 1.218370 (multi-body 3-rd order) WCORR4= 1.846150 (multi-body 4th order) WCORR5= 0.027300 (multi-body 5th order) WCORR6= 0.007410 (multi-body 6th order) WSCCOR= 1.000000 (back-scloc correlation) WTURN3= 2.913860 (turns, 3rd order) WTURN4= 0.731780 (turns, 4th order) WTURN6= 0.023910 (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= 1.000000 (SC-SC) WSCP= 2.794050 (SC-p) WELEC= 0.145810 (p-p electr) WVDWPP= 0.145810 (p-p VDW) WBOND= 1.000000 (stretching) WANG= 1.956840 (bending) WSCLOC= 0.170100 (SC local) WTOR= 2.046980 (torsional) WTORD= 1.696240 (double torsional) WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) WEL_LOC= 1.218370 (multi-body 3-rd order) WCORR4= 1.846150 (multi-body 4th order) WCORR5= 0.027300 (multi-body 5th order) WCORR6= 0.007410 (multi-body 6th order) WSCCOR= 1.000000 (back-scloc correlatkion) WTURN3= 2.913860 (turns, 3rd order) WTURN4= 0.731780 (turns, 4th order) WTURN6= 0.023910 (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 SS_DEPTH -6.90133843152500 HT 3.00000000000000 ITEL 1 10 1 2 9 1 3 9 1 4 9 1 5 1 1 6 9 1 7 9 1 8 9 1 9 9 1 10 9 1 11 9 1 12 9 1 13 9 1 14 1 1 15 9 1 16 9 1 17 9 1 ns= 2 iss: 5 14 nss= 1 ihpb,jhpb: 5 14 Boundaries in phi angle sampling: GLY 1 -180.0 180.0 ALA 2 -180.0 180.0 ALA 3 -180.0 180.0 ALA 4 -180.0 180.0 CYS 5 -180.0 180.0 ALA 6 -180.0 180.0 ALA 7 -180.0 180.0 ALA 8 -180.0 180.0 ALA 9 -180.0 180.0 ALA 10 -180.0 180.0 ALA 11 -180.0 180.0 ALA 12 -180.0 180.0 ALA 13 -180.0 180.0 CYS 14 -180.0 180.0 ALA 15 -180.0 180.0 ALA 16 -180.0 180.0 ALA 17 -180.0 180.0 GLY 18 -180.0 180.0 NZ_START= 1 NZ_END= 18 IZ_SC= 0 Processor 0 CG group 0 absolute rank 0 nhpb 1 link_start= 1 link_end 1 Initial geometry will be read in. Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.800 0.000 0.000 0.743 110.000 -120.000 ALA 3 3.800 90.000 0.000 0.743 110.000 -120.000 ALA 4 3.800 90.000 180.000 0.743 110.000 -120.000 CYS 5 3.800 90.000 180.000 1.237 100.000 -120.000 ALA 6 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 7 3.800 90.000 180.000 0.743 100.000 -120.000 ALA 8 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 9 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 10 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 11 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 12 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 13 3.800 90.000 180.000 0.743 100.000 -120.000 CYS 14 3.800 90.000 180.000 1.237 110.000 -120.000 ALA 15 3.800 90.000 180.000 0.743 100.000 -120.000 ALA 16 3.800 90.000 180.000 0.743 110.000 -120.000 ALA 17 3.800 90.000 180.000 0.743 110.000 -120.000 GLY 18 3.800 90.000 180.000 0.000 0.000 0.000 The chain contains 2 disulfide-bridging cysteines. 5 14 Pre-formed links are: CYS( 5) -- CYS( 14) 0.000 -5.500 0.000 ******************************************************************************** Processor 0: end reading molecular data. ******************************************************************************** Energy evaluation or minimization calculation. Conformations will be energy-minimized. ******************************************************************************** Time for energy evaluation 0.000000000000000E+000 Virtual-chain energies: EVDW= -1.784016E+01 WEIGHT= 1.000000E+00 (SC-SC) EVDW2= 2.118779E+01 WEIGHT= 2.794050E+00 (SC-p) EES= -8.122745E+00 WEIGHT= 1.458100E-01 (p-p) EVDWPP= -2.540621E+01 WEIGHT= 1.458100E-01 (p-p VDW) ESTR= 4.237046E-27 WEIGHT= 1.000000E+00 (stretching) EBE= -1.185178E+00 WEIGHT= 1.956840E+00 (bending) ESC= 1.520408E+02 WEIGHT= 1.701000E-01 (SC local) ETORS= 0.000000E+00 WEIGHT= 2.046980E+00 (torsional) ETORSD= -2.194244E+00 WEIGHT= 1.696240E+00 (double torsional) EHPB= 7.073396E+03 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) ECORR4= -5.324225E+00 WEIGHT= 1.846150E+00 (multi-body) ECORR5= 2.317900E+01 WEIGHT= 2.730000E-02 (multi-body) ECORR6= 1.215220E+01 WEIGHT= 7.410000E-03 (multi-body) EELLO= 3.759544E+01 WEIGHT= 1.218370E+00 (electrostatic-local) ETURN3= -3.193381E+00 WEIGHT= 2.913860E+00 (turns, 3rd order) ETURN4= 1.424793E+01 WEIGHT= 7.317800E-01 (turns, 4th order) ETURN6= 0.000000E+00 WEIGHT= 2.391000E-02 (turns, 6th order) ESCCOR= 7.779132E+00 WEIGHT= 1.000000E+00 (backbone-rotamer corr) EDIHC= 0.000000E+00 (dihedral angle constraints) ESS= -5.500000E+00 (disulfide-bridge intrinsic energy) UCONST= 0.000000E+00 (Constraint energy) ETOT= 7.175287E+03 (total) PP contact map: 1 GLY 1 ALA 3 2 ALA 2 ALA 4 3 ALA 3 CYS 5 4 ALA 4 ALA 6 5 CYS 5 ALA 7 6 ALA 6 ALA 8 7 ALA 7 ALA 9 8 ALA 8 ALA 10 9 ALA 9 ALA 11 10 ALA 10 ALA 12 11 ALA 11 ALA 13 12 ALA 12 CYS 14 13 ALA 13 ALA 15 14 CYS 14 ALA 16 15 ALA 15 ALA 17 Hairpins: Constants of electrostatic interaction energy expression. 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 Total average electrostatic energy: -1.65572537591651 VDW energy between peptide-group centers: -10.4984841780933 Electrostatic contacts before pruning: Electrostatic contacts after pruning: UNRES seq: SC_move 1120 -13.8122160409231 PP contact map: 1 ALA 4 ALA 6 2 CYS 5 ALA 7 3 ALA 6 ALA 8 4 ALA 7 ALA 9 5 ALA 8 ALA 10 6 ALA 10 ALA 12 7 ALA 13 ALA 15 Hairpins: Constants of electrostatic interaction energy expression. 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01 Total average electrostatic energy: -2.87145783452203 VDW energy between peptide-group centers: -10.1835884388674 Electrostatic contacts before pruning: 1 ALA 4 ALA 6 -0.50110 Electrostatic contacts after pruning: 1 ALA 4 ALA 6 -0.50110 UNRES seq: Virtual-chain energies: EVDW= -3.188825E+01 WEIGHT= 1.000000E+00 (SC-SC) EVDW2= 1.572209E+01 WEIGHT= 2.794050E+00 (SC-p) EES= -1.623973E+01 WEIGHT= 1.458100E-01 (p-p) EVDWPP= -2.410152E+01 WEIGHT= 1.458100E-01 (p-p VDW) ESTR= 1.688850E-01 WEIGHT= 1.000000E+00 (stretching) EBE= -1.848625E+01 WEIGHT= 1.956840E+00 (bending) ESC= -5.330904E+00 WEIGHT= 1.701000E-01 (SC local) ETORS= 1.003218E+01 WEIGHT= 2.046980E+00 (torsional) ETORSD= 4.005547E-02 WEIGHT= 1.696240E+00 (double torsional) EHPB= -1.187647E+01 WEIGHT= 1.000000E+00 (SS bridges & dist. cnstr.) ECORR4= -1.168188E+01 WEIGHT= 1.846150E+00 (multi-body) ECORR5= 6.877311E+00 WEIGHT= 2.730000E-02 (multi-body) ECORR6= 2.150591E+01 WEIGHT= 7.410000E-03 (multi-body) EELLO= 4.572045E+00 WEIGHT= 1.218370E+00 (electrostatic-local) ETURN3= 6.204726E+00 WEIGHT= 2.913860E+00 (turns, 3rd order) ETURN4= 6.693131E+00 WEIGHT= 7.317800E-01 (turns, 4th order) ETURN6= -2.421073E-01 WEIGHT= 2.391000E-02 (turns, 6th order) ESCCOR= -1.545899E+01 WEIGHT= 1.000000E+00 (backbone-rotamer corr) EDIHC= 0.000000E+00 (dihedral angle constraints) ESS= -5.500000E+00 (disulfide-bridge intrinsic energy) UCONST= 0.000000E+00 (Constraint energy) ETOT= -3.016362E+01 (total) Geometry of the virtual chain. Res d Theta Gamma Dsc Alpha Beta GLY 1 0.000 0.000 0.000 0.000 0.000 0.000 ALA 2 3.802 0.000 0.000 0.742 131.239 -75.726 ALA 3 3.807 94.222 0.000 0.742 132.313 -78.742 ALA 4 3.802 126.490 -165.860 0.743 159.389 -84.704 CYS 5 3.804 126.244 -83.777 1.237 133.758 -88.250 ALA 6 3.803 93.779 -152.942 0.742 129.396 -78.021 ALA 7 3.809 91.725 76.612 0.742 131.254 -77.909 ALA 8 3.804 93.084 81.337 0.741 136.392 -105.856 ALA 9 3.803 110.117 -98.088 0.742 139.402 -104.794 ALA 10 3.802 106.661 88.380 0.742 166.703 -78.071 ALA 11 3.801 125.157 83.555 0.741 127.223 -75.814 ALA 12 3.812 92.065 175.242 0.742 143.680 -92.666 ALA 13 3.801 121.336 81.849 0.741 167.362 -82.468 CYS 14 3.804 124.257 -82.716 1.239 129.965 -104.400 ALA 15 3.815 95.234 -174.358 0.745 144.535 -81.193 ALA 16 3.802 130.505 87.291 0.741 164.523 -79.826 ALA 17 3.804 128.136 -95.560 0.742 129.422 -76.024 GLY 18 3.808 93.035 -166.188 0.000 180.000 180.000 SUMSL return code: 4 # of energy evaluations: 952 # of energy evaluations/sec: 1457.820 CG processor 0 is finishing work. Total wall clock time 0.726562500000000 sec