--- /dev/null
+--------------------------------------------------------------------------------
+ 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
projects / unres.git / blobdiff