1. Fixed NaNs in wham (more stable computation of window free energies).
2. Minor fixes in cluster
3. Added exmaple with minimization in MD examples
1L2Y
-SEED=-3059743 PDBREF MINIMIZE
-maxmin=1000
+SEED=-3059743 REFSTR PDBREF MINIMIZE
+
WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1L2Y_minim.inp
+ Output file : 1L2Y_minim.out_GB
+
+ Sidechain potential file :
+ ../../../../PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+ 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
+ SCCOR parameter file : ../../../../PARAM/rotcorr_AM1.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
+--------------------------------------------------------------------------------
+ ### LAST MODIFIED 03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 34
+ compiled Mon Apr 2 08:16:44 2012
+ compiled by adam@matrix.chem.cornell.edu
+ OS name: Linux
+ OS release: 2.6.34.9-69.fc13.x86_64
+ OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
+ flags:
+ FC = ifort
+ 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 ...
+ CC = cc
+ CFLAGS = -DLINUX -DPGI -c
+ OPT = -O3 -ip -w
+ LIBS = -Lxdrf -lxdrf
+ 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_si...
+ 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
+ ran_num 0.930227314089531
+RMSDBC = 3.0
+RMSDBC1 = 0.5
+RMSDBC1MAX = 1.5
+DRMS = 0.1
+RMSDBCM = 3.0
+Time limit (min): 960.0
+ RESCALE_MODE 1
+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: 0.308441558441558
+ Shifting contacts: 2 2
+ 1 ILE 5 ASN 2
+ 2 TRP 7 TYR 4
+ 3 LEU 8 TYR 4
+ 4 LEU 8 ILE 5
+ 5 LYS 9 GLN 6
+ 6 GLY 12 TRP 7
+ 7 GLY 12 LEU 8
+ 8 SER 14 GLY 11
+ 9 SER 15 ASP 10
+ 10 SER 15 GLY 11
+ 11 PRO 19 TRP 7
+ 12 PRO 20 LEU 3
+ 13 PRO 20 TYR 4
+ 14 PRO 20 TRP 7
+Initial geometry will be read in.
+
+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 1.684 102.356 -82.317
+LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
+TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
+ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
+GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
+TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
+LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
+LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
+ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
+GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
+GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
+PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
+SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
+SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
+GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
+ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
+PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
+PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
+PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
+SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
+D 22 3.800 108.718 92.113 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= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
+EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -8.338619E+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= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= -7.304754E+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= -5.845169E+01 (total)
+PP contact map:
+ 1 ASN 2 TYR 4
+ 2 ASN 2 ILE 5
+ 3 LEU 3 ILE 5
+ 4 LEU 3 GLN 6
+ 5 TYR 4 GLN 6
+ 6 TYR 4 TRP 7
+ 7 TYR 4 LEU 8
+ 8 ILE 5 TRP 7
+ 9 ILE 5 LEU 8
+ 10 GLN 6 LEU 8
+ 11 GLN 6 LYS 9
+ 12 TRP 7 LYS 9
+ 13 TRP 7 ASP 10
+ 14 TRP 7 GLY 11
+ 15 TRP 7 GLY 12
+ 16 LEU 8 ASP 10
+ 17 LEU 8 GLY 11
+ 18 LYS 9 GLY 11
+ 19 ASP 10 GLY 12
+ 20 GLY 11 PRO 13
+ 21 GLY 11 SER 14
+ 22 GLY 12 SER 14
+ 23 SER 14 GLY 16
+ 24 SER 15 ARG 17
+ 25 GLY 16 PRO 18
+ 26 ARG 17 PRO 19
+ 27 PRO 18 PRO 20
+ 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: -17.0351458449875
+ VDW energy between peptide-group centers: -10.2064531653452
+
+ Electrostatic contacts before pruning:
+ 1 ASN 2 TYR 4 -1.06027
+ 2 LEU 3 ILE 5 -1.59865
+ 3 LEU 3 GLN 6 -0.54360
+ 4 TYR 4 GLN 6 -2.10033
+ 5 TYR 4 TRP 7 -0.84900
+ 6 ILE 5 TRP 7 -1.85979
+ 7 ILE 5 LEU 8 -0.53540
+ 8 GLN 6 LEU 8 -1.48363
+ 9 GLN 6 LYS 9 -0.61868
+ 10 TRP 7 LYS 9 -1.55464
+ 11 TRP 7 GLY 12 -0.37651
+ 12 LEU 8 ASP 10 -0.61626
+ 13 LEU 8 GLY 11 -0.40662
+
+ Electrostatic contacts after pruning:
+ 1 ASN 2 TYR 4 -1.06027
+ 2 LEU 3 ILE 5 -1.59865
+ 3 LEU 3 GLN 6 -0.54360
+ 4 TYR 4 GLN 6 -2.10033
+ 5 TYR 4 TRP 7 -0.84900
+ 6 ILE 5 TRP 7 -1.85979
+ 7 ILE 5 LEU 8 -0.53540
+ 8 GLN 6 LEU 8 -1.48363
+ 9 GLN 6 LYS 9 -0.61868
+ 10 TRP 7 LYS 9 -1.55464
+ 11 TRP 7 GLY 12 -0.37651
+ 12 LEU 8 ASP 10 -0.61626
+ 13 LEU 8 GLY 11 -0.40662
+Helix 1 2 10
+ UNRES seq:
+ helix 3 11
+ SC_move 1190 -14.2312827671102
+PP contact map:
+ 1 ASN 2 TYR 4
+ 2 ASN 2 ILE 5
+ 3 LEU 3 ILE 5
+ 4 LEU 3 GLN 6
+ 5 LEU 3 TRP 7
+ 6 TYR 4 GLN 6
+ 7 TYR 4 TRP 7
+ 8 TYR 4 LEU 8
+ 9 ILE 5 TRP 7
+ 10 ILE 5 LEU 8
+ 11 ILE 5 LYS 9
+ 12 GLN 6 LEU 8
+ 13 GLN 6 LYS 9
+ 14 TRP 7 LYS 9
+ 15 TRP 7 ASP 10
+ 16 TRP 7 GLY 11
+ 17 TRP 7 GLY 12
+ 18 LEU 8 ASP 10
+ 19 LEU 8 GLY 11
+ 20 LYS 9 GLY 11
+ 21 ASP 10 GLY 12
+ 22 GLY 11 PRO 13
+ 23 GLY 11 SER 14
+ 24 GLY 12 SER 14
+ 25 PRO 13 SER 15
+ 26 SER 14 GLY 16
+ 27 SER 15 ARG 17
+ 28 PRO 18 PRO 20
+ 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: -14.3281191505659
+ VDW energy between peptide-group centers: -22.1278543766753
+
+ Electrostatic contacts before pruning:
+ 1 ASN 2 TYR 4 -0.80580
+ 2 LEU 3 ILE 5 -1.08899
+ 3 LEU 3 GLN 6 -0.51166
+ 4 TYR 4 GLN 6 -1.35288
+ 5 TYR 4 TRP 7 -0.71638
+ 6 ILE 5 TRP 7 -1.25245
+ 7 ILE 5 LEU 8 -0.56094
+ 8 GLN 6 LEU 8 -1.12103
+ 9 GLN 6 LYS 9 -0.52058
+ 10 TRP 7 LYS 9 -1.15119
+ 11 LEU 8 ASP 10 -0.71444
+ 12 LEU 8 GLY 11 -0.38113
+ 13 GLY 12 SER 14 -0.61187
+
+ Electrostatic contacts after pruning:
+ 1 ASN 2 TYR 4 -0.80580
+ 2 LEU 3 ILE 5 -1.08899
+ 3 LEU 3 GLN 6 -0.51166
+ 4 TYR 4 GLN 6 -1.35288
+ 5 TYR 4 TRP 7 -0.71638
+ 6 ILE 5 TRP 7 -1.25245
+ 7 ILE 5 LEU 8 -0.56094
+ 8 GLN 6 LEU 8 -1.12103
+ 9 GLN 6 LYS 9 -0.52058
+ 10 TRP 7 LYS 9 -1.15119
+ 11 LEU 8 ASP 10 -0.71444
+ 12 LEU 8 GLY 11 -0.38113
+ 13 GLY 12 SER 14 -0.61187
+Helix 1 2 10
+ UNRES seq:
+ helix 3 11
+
+Virtual-chain energies:
+
+EVDW= -5.340090E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 4.677947E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -9.503008E+01 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= -2.608496E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -3.660091E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 8.674390E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 9.615105E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 4.819701E-01 WEIGHT= 1.570690D+00 (double torsional)
+EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -7.040856E+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= -7.334513E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= 1.856553E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= -3.312436E+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= -7.862875E+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 1.684 110.702 -85.685
+LEU 3 3.800 118.494 0.000 1.939 141.228 -49.540
+TYR 4 3.800 91.717 -100.428 2.484 118.549 113.868
+ILE 5 3.800 90.036 63.646 1.776 146.652 -96.973
+GLN 6 3.800 89.040 55.793 2.240 104.893 -50.566
+TRP 7 3.800 90.433 45.276 2.605 138.711 59.219
+LEU 8 3.800 90.769 45.241 1.939 136.395 -145.480
+LYS 9 3.800 90.500 50.320 2.541 134.179 -136.318
+ASP 10 3.800 92.103 46.289 1.709 143.475 -124.446
+GLY 11 3.800 91.360 65.751 0.000 180.000 180.000
+GLY 12 3.800 111.681 -71.670 0.000 180.000 180.000
+PRO 13 3.800 113.684 -58.655 1.345 129.775 -154.011
+SER 14 3.800 93.263 -78.152 1.150 115.010 -77.057
+SER 15 3.800 93.932 57.849 1.150 124.898 -144.294
+GLY 16 3.800 115.865 137.415 0.000 180.000 180.000
+ARG 17 3.800 94.303 -84.359 3.020 90.176 -107.687
+PRO 18 3.800 121.756 61.635 1.345 116.339 -177.378
+PRO 19 3.800 117.856 -81.085 1.345 141.987 -158.715
+PRO 20 3.800 115.623 -108.327 1.345 97.877 -97.653
+SER 21 3.800 93.855 -137.450 1.150 144.130 -129.546
+D 22 3.800 117.793 46.049 0.000 180.000 180.000
+RMS deviation from the reference structure: 2.067
+ % of native contacts: 78.571
+ % of nonnative contacts: 54.167
+ contact order: 0.348
+SUMSL return code: 4
+# of energy evaluations: 348
+# of energy evaluations/sec: 3154.545
+
+
+***** Computation time: 0 hours 0 minutes 0 seconds *****
--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1L2Y_minim.inp
+ Output file : 1L2Y_minim.out_GB000
+
+ 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 - parallel job.
+********************************************************************************
+ ### LAST MODIFIED 03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 62
+ compiled Sun May 13 16:07:22 2012
+ compiled by adam@matrix.chem.cornell.edu
+ OS name: Linux
+ OS release: 2.6.34.9-69.fc13.x86_64
+ OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
+ 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 -46
+ -45086
+ 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 1
+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: 0.308441558441558
+ Shifting contacts: 2 2
+ 1 ILE 5 ASN 2
+ 2 TRP 7 TYR 4
+ 3 LEU 8 TYR 4
+ 4 LEU 8 ILE 5
+ 5 LYS 9 GLN 6
+ 6 GLY 12 TRP 7
+ 7 GLY 12 LEU 8
+ 8 SER 14 GLY 11
+ 9 SER 15 ASP 10
+ 10 SER 15 GLY 11
+ 11 PRO 19 TRP 7
+ 12 PRO 20 LEU 3
+ 13 PRO 20 TYR 4
+ 14 PRO 20 TRP 7
+Initial geometry will be read in.
+
+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 1.684 102.356 -82.317
+LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
+TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
+ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
+GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
+TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
+LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
+LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
+ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
+GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
+GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
+PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
+SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
+SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
+GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
+ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
+PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
+PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
+PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
+SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
+D 22 3.800 108.718 92.113 0.000 0.000 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= -4.954316E+01 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -8.338619E+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= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= -7.304754E+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= -5.845169E+01 (total)
+PP contact map:
+ 1 ASN 2 TYR 4
+ 2 ASN 2 ILE 5
+ 3 LEU 3 ILE 5
+ 4 LEU 3 GLN 6
+ 5 TYR 4 GLN 6
+ 6 TYR 4 TRP 7
+ 7 TYR 4 LEU 8
+ 8 ILE 5 TRP 7
+ 9 ILE 5 LEU 8
+ 10 GLN 6 LEU 8
+ 11 GLN 6 LYS 9
+ 12 TRP 7 LYS 9
+ 13 TRP 7 ASP 10
+ 14 TRP 7 GLY 11
+ 15 TRP 7 GLY 12
+ 16 LEU 8 ASP 10
+ 17 LEU 8 GLY 11
+ 18 LYS 9 GLY 11
+ 19 ASP 10 GLY 12
+ 20 GLY 11 PRO 13
+ 21 GLY 11 SER 14
+ 22 GLY 12 SER 14
+ 23 SER 14 GLY 16
+ 24 SER 15 ARG 17
+ 25 GLY 16 PRO 18
+ 26 ARG 17 PRO 19
+ 27 PRO 18 PRO 20
+ 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: -17.0351458449875
+ VDW energy between peptide-group centers: -10.2064531653452
+
+ Electrostatic contacts before pruning:
+ 1 ASN 2 TYR 4 -1.06027
+ 2 LEU 3 ILE 5 -1.59865
+ 3 LEU 3 GLN 6 -0.54360
+ 4 TYR 4 GLN 6 -2.10033
+ 5 TYR 4 TRP 7 -0.84900
+ 6 ILE 5 TRP 7 -1.85979
+ 7 ILE 5 LEU 8 -0.53540
+ 8 GLN 6 LEU 8 -1.48363
+ 9 GLN 6 LYS 9 -0.61868
+ 10 TRP 7 LYS 9 -1.55464
+ 11 TRP 7 GLY 12 -0.37651
+ 12 LEU 8 ASP 10 -0.61626
+ 13 LEU 8 GLY 11 -0.40662
+
+ Electrostatic contacts after pruning:
+ 1 ASN 2 TYR 4 -1.06027
+ 2 LEU 3 ILE 5 -1.59865
+ 3 LEU 3 GLN 6 -0.54360
+ 4 TYR 4 GLN 6 -2.10033
+ 5 TYR 4 TRP 7 -0.84900
+ 6 ILE 5 TRP 7 -1.85979
+ 7 ILE 5 LEU 8 -0.53540
+ 8 GLN 6 LEU 8 -1.48363
+ 9 GLN 6 LYS 9 -0.61868
+ 10 TRP 7 LYS 9 -1.55464
+ 11 TRP 7 GLY 12 -0.37651
+ 12 LEU 8 ASP 10 -0.61626
+ 13 LEU 8 GLY 11 -0.40662
+Helix 1 2 10
+ UNRES seq:
+ helix 3 11
+ SC_move 1190 -36.8538206659302
+PP contact map:
+ 1 ASN 2 TYR 4
+ 2 ASN 2 ILE 5
+ 3 LEU 3 ILE 5
+ 4 LEU 3 GLN 6
+ 5 LEU 3 TRP 7
+ 6 LEU 3 LEU 8
+ 7 TYR 4 GLN 6
+ 8 TYR 4 TRP 7
+ 9 TYR 4 LEU 8
+ 10 ILE 5 TRP 7
+ 11 ILE 5 LEU 8
+ 12 ILE 5 LYS 9
+ 13 GLN 6 LEU 8
+ 14 GLN 6 LYS 9
+ 15 TRP 7 LYS 9
+ 16 TRP 7 ASP 10
+ 17 TRP 7 GLY 11
+ 18 TRP 7 GLY 12
+ 19 LEU 8 ASP 10
+ 20 LEU 8 GLY 11
+ 21 LEU 8 GLY 12
+ 22 LYS 9 GLY 11
+ 23 ASP 10 GLY 12
+ 24 ASP 10 PRO 13
+ 25 ASP 10 SER 14
+ 26 GLY 11 PRO 13
+ 27 GLY 11 SER 14
+ 28 GLY 12 SER 14
+ 29 PRO 13 SER 15
+ 30 SER 14 GLY 16
+ 31 SER 15 ARG 17
+ 32 PRO 18 PRO 20
+ 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: -37.0692889481661
+ VDW energy between peptide-group centers: 851.859545972044
+
+ Electrostatic contacts before pruning:
+ 1 ASN 2 TYR 4 -9.86113
+ 2 ASN 2 ILE 5 -1.53124
+ 3 LEU 3 ILE 5 -10.58267
+ 4 LEU 3 GLN 6 -1.25110
+ 5 LEU 3 TRP 7 -0.80052
+ 6 TYR 4 GLN 6 -1.33813
+ 7 TYR 4 TRP 7 -0.75936
+ 8 ILE 5 TRP 7 -1.25974
+ 9 ILE 5 LEU 8 -0.55583
+ 10 GLN 6 LEU 8 -1.12670
+ 11 GLN 6 LYS 9 -0.55504
+ 12 TRP 7 LYS 9 -1.20931
+ 13 TRP 7 GLY 12 -0.39500
+ 14 LEU 8 ASP 10 -0.66375
+ 15 LEU 8 GLY 11 -0.49451
+ 16 ASP 10 SER 14 -0.49993
+ 17 GLY 11 PRO 13 -0.96815
+
+ Electrostatic contacts after pruning:
+ 1 ASN 2 TYR 4 -9.86113
+ 2 ASN 2 ILE 5 -1.53124
+ 3 LEU 3 ILE 5 -10.58267
+ 4 LEU 3 GLN 6 -1.25110
+ 5 LEU 3 TRP 7 -0.80052
+ 6 TYR 4 GLN 6 -1.33813
+ 7 TYR 4 TRP 7 -0.75936
+ 8 ILE 5 TRP 7 -1.25974
+ 9 ILE 5 LEU 8 -0.55583
+ 10 GLN 6 LEU 8 -1.12670
+ 11 GLN 6 LYS 9 -0.55504
+ 12 TRP 7 LYS 9 -1.20931
+ 13 TRP 7 GLY 12 -0.39500
+ 14 LEU 8 ASP 10 -0.66375
+ 15 LEU 8 GLY 11 -0.49451
+ 16 ASP 10 SER 14 -0.49993
+ 17 GLY 11 PRO 13 -0.96815
+Helix 1 3 10
+ UNRES seq:
+ helix 4 11
+
+Virtual-chain energies:
+
+EVDW= 1.906975E+22 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 2.099470E+04 WEIGHT= 1.593040D+00 (SC-p)
+EES= -2.515997E+02 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= 2.987216E+03 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -9.194128E+00 WEIGHT= 1.138730D+00 (bending)
+ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 8.926809E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= -4.669374E-01 WEIGHT= 1.570690D+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -1.345056E+02 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= NaN WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= NaN 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= 1.000000E+99 (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 66.094 -81.746
+LEU 3 3.800 118.689 0.000 1.939 138.109 -26.893
+TYR 4 3.800 91.783 -149.590 2.484 123.984 108.154
+ILE 5 3.800 0.000 84.251 1.776 149.498 -90.988
+GLN 6 3.800 90.614 45.428 2.240 118.674 -118.972
+TRP 7 3.800 90.358 42.479 2.605 163.095 48.723
+LEU 8 3.800 90.561 45.576 1.939 145.280 -129.675
+LYS 9 3.800 90.389 50.728 2.541 133.176 -134.505
+ASP 10 3.800 91.852 44.664 1.709 133.932 -129.183
+GLY 11 3.800 90.570 70.394 0.000 180.000 180.000
+GLY 12 3.800 105.668 -67.487 0.000 180.000 180.000
+PRO 13 3.800 99.159 -65.573 1.345 115.572 -113.582
+SER 14 3.800 92.474 -33.144 1.150 113.504 -79.318
+SER 15 3.800 94.029 101.491 1.150 124.420 -158.647
+GLY 16 3.800 115.039 122.531 0.000 180.000 180.000
+ARG 17 3.800 94.980 -88.208 3.020 101.436 -102.179
+PRO 18 3.800 125.046 63.779 1.345 121.700 -130.547
+PRO 19 3.800 117.245 -83.662 1.345 110.939 -109.306
+PRO 20 3.800 121.153 -109.808 1.345 105.368 -111.814
+SER 21 3.800 92.281 -149.201 1.150 124.532 -120.711
+D 22 3.800 116.744 105.020 0.000 180.000 180.000
+RMS deviation from the reference structure: 2.344
+ % of native contacts: 64.286
+ % of nonnative contacts: 57.143
+ contact order: 0.253
+SUMSL return code: 4
+# of energy evaluations: 553
+# of energy evaluations/sec: 3072.000
+CG processor 0 is finishing work.
+ Total wall clock time 0.242187500000000 sec
--- /dev/null
+--------------------------------------------------------------------------------
+ FILE ASSIGNMENT
+--------------------------------------------------------------------------------
+ Input file : 1L2Y_minim.inp
+ Output file : 1L2Y_minim.out_LJ000
+
+ Sidechain potential file : /users/adam/UNRES/PARAM/scinter_LJ.parm
+ 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 - parallel job.
+********************************************************************************
+ ### LAST MODIFIED 03/28/12 23:29 by czarek
+ ++++ Compile info ++++
+ Version 2.5 build 62
+ compiled Sun May 13 16:07:22 2012
+ compiled by adam@matrix.chem.cornell.edu
+ OS name: Linux
+ OS release: 2.6.34.9-69.fc13.x86_64
+ OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
+ 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 LJ , 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 -46
+ -45086
+ 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 1
+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: 0.320158102766798
+ Shifting contacts: 2 2
+ 1 ILE 5 ASN 2
+ 2 TRP 7 TYR 4
+ 3 LEU 8 TYR 4
+ 4 LEU 8 ILE 5
+ 5 LYS 9 GLN 6
+ 6 GLY 11 TRP 7
+ 7 GLY 11 LEU 8
+ 8 GLY 12 TRP 7
+ 9 GLY 12 LEU 8
+ 10 PRO 13 TRP 7
+ 11 SER 14 GLY 11
+ 12 SER 15 TRP 7
+ 13 SER 15 ASP 10
+ 14 SER 15 GLY 11
+ 15 SER 15 GLY 12
+ 16 ARG 17 TRP 7
+ 17 ARG 17 ASP 10
+ 18 PRO 18 TRP 7
+ 19 PRO 19 TYR 4
+ 20 PRO 19 TRP 7
+ 21 PRO 20 LEU 3
+ 22 PRO 20 TYR 4
+ 23 PRO 20 TRP 7
+Initial geometry will be read in.
+
+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 1.684 102.356 -82.317
+LEU 3 3.800 104.929 0.000 1.939 120.092 -56.685
+TYR 4 3.800 87.695 -100.430 2.484 152.364 85.090
+ILE 5 3.800 81.904 72.426 1.776 134.976 -88.666
+GLN 6 3.800 82.466 66.026 2.240 122.343 -140.945
+TRP 7 3.800 84.466 51.434 2.605 152.178 38.024
+LEU 8 3.800 83.945 53.508 1.939 159.052 179.471
+LYS 9 3.800 85.396 60.569 2.541 100.558 -73.090
+ASP 10 3.800 91.449 44.177 1.709 139.961 -144.797
+GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
+GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
+PRO 13 3.800 119.363 -61.916 1.345 117.453 -133.163
+SER 14 3.800 94.363 -75.894 1.150 137.025 -106.659
+SER 15 3.800 96.264 67.358 1.150 146.290 -130.305
+GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
+ARG 17 3.800 96.299 -95.571 3.020 93.901 -102.747
+PRO 18 3.800 129.702 63.972 1.345 101.025 -111.641
+PRO 19 3.800 109.445 -74.504 1.345 113.043 -122.044
+PRO 20 3.800 106.349 -122.306 1.345 93.778 -102.374
+SER 21 3.800 106.042 -134.605 1.150 153.835 -143.303
+D 22 3.800 108.718 92.113 0.000 0.000 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= 6.950763E+00 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 5.228224E+01 WEIGHT= 1.593040D+00 (SC-p)
+EES= -1.132072E+02 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= 2.375178E+01 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -1.651995E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 7.185904E+01 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 8.243370E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 2.390466E+00 WEIGHT= 1.570690D+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -8.338619E+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= -5.753258E+00 WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= 1.901845E+01 WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= -7.304754E+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= 1.797273E+01 (total)
+PP contact map:
+ 1 ASN 2 TYR 4
+ 2 ASN 2 ILE 5
+ 3 LEU 3 ILE 5
+ 4 LEU 3 GLN 6
+ 5 TYR 4 GLN 6
+ 6 TYR 4 TRP 7
+ 7 TYR 4 LEU 8
+ 8 ILE 5 TRP 7
+ 9 ILE 5 LEU 8
+ 10 GLN 6 LEU 8
+ 11 GLN 6 LYS 9
+ 12 TRP 7 LYS 9
+ 13 TRP 7 ASP 10
+ 14 TRP 7 GLY 11
+ 15 TRP 7 GLY 12
+ 16 LEU 8 ASP 10
+ 17 LEU 8 GLY 11
+ 18 LYS 9 GLY 11
+ 19 ASP 10 GLY 12
+ 20 GLY 11 PRO 13
+ 21 GLY 11 SER 14
+ 22 GLY 12 SER 14
+ 23 SER 14 GLY 16
+ 24 SER 15 ARG 17
+ 25 GLY 16 PRO 18
+ 26 ARG 17 PRO 19
+ 27 PRO 18 PRO 20
+ 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: -17.0351458449875
+ VDW energy between peptide-group centers: -10.2064531653452
+
+ Electrostatic contacts before pruning:
+ 1 ASN 2 TYR 4 -1.06027
+ 2 LEU 3 ILE 5 -1.59865
+ 3 LEU 3 GLN 6 -0.54360
+ 4 TYR 4 GLN 6 -2.10033
+ 5 TYR 4 TRP 7 -0.84900
+ 6 ILE 5 TRP 7 -1.85979
+ 7 ILE 5 LEU 8 -0.53540
+ 8 GLN 6 LEU 8 -1.48363
+ 9 GLN 6 LYS 9 -0.61868
+ 10 TRP 7 LYS 9 -1.55464
+ 11 TRP 7 GLY 12 -0.37651
+ 12 LEU 8 ASP 10 -0.61626
+ 13 LEU 8 GLY 11 -0.40662
+
+ Electrostatic contacts after pruning:
+ 1 ASN 2 TYR 4 -1.06027
+ 2 LEU 3 ILE 5 -1.59865
+ 3 LEU 3 GLN 6 -0.54360
+ 4 TYR 4 GLN 6 -2.10033
+ 5 TYR 4 TRP 7 -0.84900
+ 6 ILE 5 TRP 7 -1.85979
+ 7 ILE 5 LEU 8 -0.53540
+ 8 GLN 6 LEU 8 -1.48363
+ 9 GLN 6 LYS 9 -0.61868
+ 10 TRP 7 LYS 9 -1.55464
+ 11 TRP 7 GLY 12 -0.37651
+ 12 LEU 8 ASP 10 -0.61626
+ 13 LEU 8 GLY 11 -0.40662
+Helix 1 2 10
+ UNRES seq:
+ helix 3 11
+ SC_move 1189 -4.13326717681629
+PP contact map:
+ 1 ASN 2 TYR 4
+ 2 ASN 2 ILE 5
+ 3 LEU 3 ILE 5
+ 4 LEU 3 GLN 6
+ 5 LEU 3 TRP 7
+ 6 TYR 4 GLN 6
+ 7 TYR 4 TRP 7
+ 8 ILE 5 TRP 7
+ 9 ILE 5 LEU 8
+ 10 GLN 6 LEU 8
+ 11 GLN 6 LYS 9
+ 12 TRP 7 LYS 9
+ 13 TRP 7 ASP 10
+ 14 TRP 7 GLY 11
+ 15 TRP 7 GLY 12
+ 16 LEU 8 ASP 10
+ 17 LEU 8 GLY 11
+ 18 LYS 9 GLY 11
+ 19 ASP 10 GLY 12
+ 20 GLY 11 PRO 13
+ 21 GLY 11 SER 14
+ 22 GLY 12 SER 14
+ 23 PRO 13 SER 15
+ 24 PRO 13 PRO 18
+ 25 SER 14 GLY 16
+ 26 SER 14 ARG 17
+ 27 SER 15 ARG 17
+ 28 PRO 18 PRO 20
+ 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: -34.0939296423320
+ VDW energy between peptide-group centers: 899.113237730561
+
+ Electrostatic contacts before pruning:
+ 1 ASN 2 TYR 4 -10.17518
+ 2 ASN 2 ILE 5 -1.20257
+ 3 LEU 3 ILE 5 -10.90405
+ 4 LEU 3 GLN 6 -1.04733
+ 5 LEU 3 TRP 7 -0.51328
+ 6 TYR 4 GLN 6 -1.11943
+ 7 TYR 4 TRP 7 -0.47363
+ 8 ILE 5 TRP 7 -1.27116
+ 9 GLN 6 LEU 8 -0.57639
+ 10 TRP 7 LYS 9 -1.27183
+ 11 TRP 7 ASP 10 -0.33671
+ 12 LEU 8 ASP 10 -0.74960
+ 13 LEU 8 GLY 11 -0.44794
+ 14 GLY 12 SER 14 -0.51788
+
+ Electrostatic contacts after pruning:
+ 1 ASN 2 TYR 4 -10.17518
+ 2 ASN 2 ILE 5 -1.20257
+ 3 LEU 3 ILE 5 -10.90405
+ 4 LEU 3 GLN 6 -1.04733
+ 5 LEU 3 TRP 7 -0.51328
+ 6 TYR 4 GLN 6 -1.11943
+ 7 TYR 4 TRP 7 -0.47363
+ 8 ILE 5 TRP 7 -1.27116
+ 9 GLN 6 LEU 8 -0.57639
+ 10 TRP 7 LYS 9 -1.27183
+ 11 TRP 7 ASP 10 -0.33671
+ 12 LEU 8 ASP 10 -0.74960
+ 13 LEU 8 GLY 11 -0.44794
+ 14 GLY 12 SER 14 -0.51788
+Helix 1 1 7
+ UNRES seq:
+ helix 2 8
+
+Virtual-chain energies:
+
+EVDW= 6.783553E+02 WEIGHT= 1.352790D+00 (SC-SC)
+EVDW2= 2.098526E+04 WEIGHT= 1.593040D+00 (SC-p)
+EES= -2.316959E+02 WEIGHT= 7.153400D-01 (p-p)
+EVDWPP= 3.102288E+03 WEIGHT= 1.137100D-01 (p-p VDW)
+ESTR= 6.779273E-27 WEIGHT= 1.000000D+00 (stretching)
+EBE= -1.030472E+01 WEIGHT= 1.138730D+00 (bending)
+ESC= 5.035340E+32 WEIGHT= 1.625800D-01 (SC local)
+ETORS= 8.256991E+00 WEIGHT= 1.985990D+00 (torsional)
+ETORSD= 1.541091E+00 WEIGHT= 1.570690D+00 (double torsional)
+EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
+ECORR4= -1.142431E+02 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= NaN WEIGHT= 1.603600D-01 (electrostatic-local)
+ETURN3= NaN WEIGHT= 1.687220D+00 (turns, 3rd order)
+ETURN4= NaN 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= 1.000000E+99 (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 1.684 166.403 -78.295
+LEU 3 3.800 118.535 0.000 1.939 98.410 -20.526
+TYR 4 3.800 91.262 -84.783 2.484 143.962 -14.485
+ILE 5 3.800 0.000 74.731 1.776 126.981 -107.717
+GLN 6 3.800 90.125 49.156 2.240 123.165 -131.319
+TRP 7 3.800 89.563 53.467 2.605 136.415 -30.509
+LEU 8 3.800 89.157 49.735 1.939 155.047 -119.048
+LYS 9 3.800 90.266 80.355 2.541 138.316 -137.964
+ASP 10 3.800 91.711 42.732 1.709 143.742 -133.222
+GLY 11 3.800 91.876 63.556 0.000 180.000 180.000
+GLY 12 3.800 115.894 -57.622 0.000 180.000 180.000
+PRO 13 3.800 120.076 -75.407 1.345 106.478 -96.392
+SER 14 3.800 92.479 -68.391 1.150 133.923 -99.369
+SER 15 3.800 94.169 65.963 1.150 114.383 -74.889
+GLY 16 3.800 93.692 138.023 0.000 180.000 180.000
+ARG 17 3.800 94.409 -73.682 3.020 95.051 -65.680
+PRO 18 3.800 130.488 58.633 1.345 120.711 -129.430
+PRO 19 3.800 117.860 -103.495 1.345 125.023 -135.544
+PRO 20 3.800 116.631 -108.533 1.345 97.647 -118.910
+SER 21 3.800 93.213 -137.715 1.150 119.341 -84.219
+D 22 3.800 120.091 73.011 0.000 180.000 180.000
+RMS deviation from the reference structure: 2.378
+ % of native contacts: 60.870
+ % of nonnative contacts: 39.130
+ contact order: 0.300
+SUMSL return code: 4
+# of energy evaluations: 431
+# of energy evaluations/sec: 3335.758
+CG processor 0 is finishing work.
+ Total wall clock time 0.195312500000000 sec
--- /dev/null
+ 0 -78.629 0
+ 118.4938 91.7167 90.0355 89.0402 90.4331 90.7695 90.5004 92.1025
+ 91.3597 111.6806 113.6844 93.2625 93.9321 115.8645 94.3034 121.7562
+ 117.8557 115.6233 93.8548 117.7927
+ -100.4277 63.6464 55.7934 45.2757 45.2407 50.3196 46.2887 65.7510
+ -71.6699 -58.6548 -78.1521 57.8486 137.4148 -84.3592 61.6350 -81.0853
+ -108.3267 -137.4501 46.0495
+ 110.7016 141.2278 118.5494 146.6522 104.8935 138.7112 136.3949 134.1788
+ 143.4752 180.0000 180.0000 129.7747 115.0099 124.8976 180.0000 90.1761
+ 116.3394 141.9872 97.8769 144.1295
+ -85.6852 -49.5399 113.8683 -96.9727 -50.5662 59.2188 -145.4804 -136.3182
+ -124.4460 180.0000 180.0000 -154.0107 -77.0566 -144.2941 180.0000 -107.6874
+ -177.3783 -158.7148 -97.6530 -129.5456
--- /dev/null
+ 0************ 0
+ 118.6889 91.7826 0.0000 90.6142 90.3584 90.5610 90.3893 91.8517
+ 90.5697 105.6675 99.1585 92.4742 94.0291 115.0390 94.9803 125.0459
+ 117.2452 121.1533 92.2810 116.7440
+ -149.5898 84.2508 45.4276 42.4792 45.5761 50.7277 44.6644 70.3941
+ -67.4870 -65.5727 -33.1437 101.4914 122.5310 -88.2079 63.7788 -83.6619
+ -109.8078 -149.2012 105.0201
+ 66.0940 138.1088 123.9842 149.4976 118.6739 163.0952 145.2796 133.1762
+ 133.9319 180.0000 180.0000 115.5719 113.5038 124.4199 180.0000 101.4361
+ 121.6996 110.9385 105.3684 124.5323
+ -81.7460 -26.8931 108.1542 -90.9882 -118.9725 48.7228 -129.6748 -134.5051
+ -129.1828 180.0000 180.0000 -113.5817 -79.3178 -158.6472 180.0000 -102.1785
+ -130.5467 -109.3060 -111.8144 -120.7112
--- /dev/null
+ 0************ 0
+ 118.5349 91.2615 0.0000 90.1249 89.5628 89.1570 90.2660 91.7107
+ 91.8763 115.8941 120.0758 92.4795 94.1689 93.6918 94.4088 130.4883
+ 117.8596 116.6312 93.2127 120.0906
+ -84.7829 74.7307 49.1557 53.4670 49.7352 80.3551 42.7322 63.5565
+ -57.6216 -75.4075 -68.3913 65.9628 138.0231 -73.6821 58.6330 -103.4954
+ -108.5326 -137.7154 73.0113
+ 166.4029 98.4096 143.9619 126.9814 123.1648 136.4149 155.0468 138.3159
+ 143.7423 180.0000 180.0000 106.4783 133.9230 114.3826 180.0000 95.0507
+ 120.7111 125.0235 97.6472 119.3410
+ -78.2954 -20.5265 -14.4853 -107.7166 -131.3195 -30.5095 -119.0482 -137.9641
+ -133.2218 180.0000 180.0000 -96.3923 -99.3690 -74.8894 180.0000 -65.6796
+ -129.4301 -135.5437 -118.9101 -84.2187
--- /dev/null
+DefPropRes 'helix1' 'num = 2.. 9'
+DefPropRes 'helix' 'helix1'
+DefPropRes 'coil' '! (helix | sheet)'
+XMacStand ribbon.mac
+DefPropRes 'helix1' 'num = 3.. 9'
+DefPropRes 'helix' 'helix1'
+DefPropRes 'coil' '! (helix | sheet)'
+XMacStand ribbon.mac
--- /dev/null
+#PBS -N test
+#PBS -q dque
+#PBS -l nodes=1:ppn=1
+#PBS -l mem=2gb
+#PBS -l walltime=24:00:00
+
+setenv MPIRUN "/users/software/mpich-1.2.7p1_intel-10.1_em64_ssh/bin/mpirun "
+setenv NPROCS `cat $PBS_NODEFILE | wc -l`
+
+cd $PBS_O_WORKDIR
+$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS ./unres.csh
+
--- /dev/null
+Bye Bye...
--- /dev/null
+Bye Bye...
--- /dev/null
+ Processor 0 out of 1 rank in CG_COMM 0
+ size of CG_COMM 1 size of FG_COMM 1 rank in FG_COMM1
+ 0 size of FG_COMM1 1
+Inside initialize MPI: node= 0 iseed(4)= 0 0 -46
+ -45086
+ indpdb= 0 pdbref= T
+ Call Read_Bridge.
+ ns= 0
+ Processor 0 0 0 ivec_start 1 ivec_end
+ 21
+ after etotal
+ Calling OVERLAP_SC
+ SC_move 1189 -4.13326717681629
+ Calling MINIMIZE.
+ SUMSL return code is 4 eval 430
+ # eval/s 3335.75757575758
+ refstr= T
+CG processor 0 is finishing work.
+--------------------------------------
+Running PBS epilogue script
+
+Single processor job or ~/.nokill exist, no need to kill processes
+Done.
--- /dev/null
+ Processor 0 out of 1 rank in CG_COMM 0
+ size of CG_COMM 1 size of FG_COMM 1 rank in FG_COMM1
+ 0 size of FG_COMM1 1
+Inside initialize MPI: node= 0 iseed(4)= 0 0 -46
+ -45086
+ indpdb= 0 pdbref= T
+ Call Read_Bridge.
+ ns= 0
+ Processor 0 0 0 ivec_start 1 ivec_end
+ 21
+ after etotal
+ Calling OVERLAP_SC
+ SC_move 1190 -36.8538206659302
+ Calling MINIMIZE.
+ SUMSL return code is 4 eval 552
+ # eval/s 3072.00000000000
+ refstr= T
+CG processor 0 is finishing work.
+--------------------------------------
+Running PBS epilogue script
+
+Single processor job or ~/.nokill exist, no need to kill processes
+Done.
--- /dev/null
+#!/bin/csh -f
+# Script to run the program unresCSA on linux with MPICH/PBS (parallel version).
+#
+
+setenv OUT1FILE YES
+setenv FGPROCS 1
+setenv POT GB
+setenv PREFIX 1L2Y_minim
+
+set DD = /users/adam/UNRES/PARAM
+setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_MPICH_GAB.exe
+#setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_single_GAB.exe
+#---------------------------------
+setenv BONDPAR $DD/bond.parm
+setenv THETPAR $DD/thetaml.5parm
+setenv ROTPAR $DD/scgauss.parm
+setenv TORPAR $DD/torsion_631Gdp.parm
+setenv TORDPAR $DD/torsion_double_631Gdp.parm
+setenv ELEPAR $DD/electr_631Gdp.parm
+setenv SIDEPAR ${DD}/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+#setenv SIDEPAR ${DD}/scinter_LJ.parm
+setenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3
+setenv SCPPAR $DD/scp.parm
+setenv SCCORPAR $DD/rotcorr_AM1.parm
+
+# Pattern database
+setenv PATTERN $DD/patterns.cart
+#--------------------------------------------
+
+$UNRES_BIN $*
+
export POT=$1
export PREFIX=$2
#-----------------------------------------------------------------------------
-UNRES_BIN=../../../../bin/unres/MD/unres_gfortran_single.exe
+UNRES_BIN=../../../../bin/unres/MD/unres_ifort_single_GAB.exe
#-----------------------------------------------------------------------------
-DD=../../PARAM
+DD=../../../../PARAM
export BONDPAR=$DD/bond.parm
export THETPAR=$DD/thetaml.5parm
export ROTPAR=$DD/scgauss.parm
export SIDEPAR=$DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
export FOURIER=$DD/fourier_opt.parm.1igd_hc_iter3_3
export SCPPAR=$DD/scp.parm
+export SCCORPAR=$DD/rotcorr_AM1.parm
export PATTERN=$DD/patterns.cart
#-----------------------------------------------------------------------------
$UNRES_BIN
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 0 546
+C 0 0 565
subroutine cinfo
include 'COMMON.IOUNITS'
write(iout,*)'++++ Compile info ++++'
- write(iout,*)'Version 0.0 build 546'
- write(iout,*)'compiled Sun May 20 07:28:19 2012'
+ write(iout,*)'Version 0.0 build 565'
+ write(iout,*)'compiled Tue May 29 04:48:26 2012'
write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
write(iout,*)'OS name: Linux '
write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
parameter (MaxPoint=MaxStr,
& MaxPointProc=MaxStr_Proc)
double precision finorm_max,potfac,entmin,entmax,expfac,vf
+ double precision entfac_min,entfac_min_t
parameter (finorm_max=1.0d0)
integer islice
integer i,ii,j,jj,k,kk,l,m,ind,iter,t,tmax,ient,ientmax,iln
double precision energia(0:max_ene)
#ifdef MPI
integer tmax_t,upindE_p
- double precision fi_p(MaxR,MaxT_h,Max_Parm)
+ double precision fi_p(MaxR,MaxT_h,Max_Parm),
+ & fi_p_min(MaxR,MaxT_h,Max_Parm)
double precision sumW_p(0:Max_GridT,Max_Parm),
& sumE_p(0:Max_GridT,Max_Parm),sumEsq_p(0:Max_GridT,Max_Parm),
& sumQ_p(MaxQ1,0:Max_GridT,Max_Parm),
& sumEprim(0:NGridT,Max_Parm),sumEbis(0:NGridT,Max_Parm),betaT,
& weight,econstr
double precision fi(MaxR,maxT_h,Max_Parm),
+ & fi_min(MaxR,maxT_h,Max_Parm),
& dd,dd1,dd2,hh,dmin,denom,finorm,avefi,pom,
& hfin(0:MaxHdim,maxT_h),histE(0:maxindE),
& hrmsrgy(0:MaxBinRgy,0:MaxBinRms,maxT_h),
! Compute new free-energy values corresponding to the righ-hand side of the
! equation and their derivatives.
write (iout,*) "------------------------fi"
+ entfac_min=1.0d10
#ifdef MPI
do t=1,scount(me1)
#else
enddo
enddo
entfac(t)=-dlog(denom)-vmax
+ if (entfac(t).lt.entfac_min) entfac_min=entfac(t)
#ifdef DEBUG
write (iout,*) t,"vmax",vmax," denom",denom,"entfac",entfac(t)
#endif
enddo
+c#ifdef MPI
+c write (iout,*) "entfac_min before AllReduce",entfac_min
+c call MPI_AllReduce(entfac_min,entfac_min_t,1,
+c & MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR)
+c entfac_min=entfac_min_t
+c write (iout,*) "entfac_min after AllReduce",entfac_min
+c#endif
+c#ifdef MPI
+c do t=1,scount(me)
+c entfac(t)=entfac(t)-entfac_min
+c enddo
+c#else
+c do t=1,ntot(islice)
+c entfac(t)=entfac(t)-entfac_min
+c enddo
+c#endif
+ do iparm=1,nParmSet
+ do iib=1,nT_h(iparm)
+ do ii=1,nR(iib,iparm)
+#ifdef MPI
+ fi_p_min(ii,iib,iparm)=-1.0d10
+ do t=1,scount(me)
+ aux=v(t,ii,iib,iparm)+entfac(t)
+ if (aux.gt.fi_p_min(ii,iib,iparm))
+ & fi_p_min(ii,iib,iparm)=aux
+ enddo
+#else
+ do t=1,ntot(islice)
+ aux=v(t,ii,iib,iparm)+entfac(t)
+ if (aux.gt.fi_min(ii,iib,iparm))
+ & fi_min(ii,iib,iparm)=aux
+ enddo
+#endif
+ enddo ! ii
+ enddo ! iib
+ enddo ! iparm
+#ifdef MPI
+#ifdef DEBUG
+ write (iout,*) "fi_min before AllReduce"
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ write (iout,*) (i,j,k,fi_p_min(k,j,i),k=1,nR(j,i))
+ enddo
+ enddo
+#endif
+ call MPI_AllReduce(fi_p_min,fi_min,MaxR*MaxT_h*nParmSet,
+ & MPI_DOUBLE_PRECISION,MPI_MAX,WHAM_COMM,IERROR)
+#ifdef DEBUG
+ write (iout,*) "fi_min after AllReduce"
+ do i=1,nParmSet
+ do j=1,nT_h(i)
+ write (iout,*) (i,j,k,fi_min(k,j,i),k=1,nR(j,i))
+ enddo
+ enddo
+#endif
+#endif
do iparm=1,nParmSet
do iib=1,nT_h(iparm)
do ii=1,nR(iib,iparm)
fi_p(ii,iib,iparm)=0.0d0
do t=1,scount(me)
fi_p(ii,iib,iparm)=fi_p(ii,iib,iparm)
- & +dexp(v(t,ii,iib,iparm)+entfac(t))
+ & +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm))
#ifdef DEBUG
- write (iout,'(4i5,3e15.5)') t,ii,iib,iparm,
- & v(t,ii,iib,iparm),entfac(t),fi_p(ii,iib,iparm)
+ write (iout,'(4i5,4e15.5)') t,ii,iib,iparm,
+ & v(t,ii,iib,iparm),entfac(t),fi_min(ii,iib,iparm),
+ & fi_p(ii,iib,iparm)
#endif
enddo
#else
fi(ii,iib,iparm)=0.0d0
do t=1,ntot(islice)
fi(ii,iib,iparm)=fi(ii,iib,iparm)
- & +dexp(v(t,ii,iib,iparm)+entfac(t))
+ & +dexp(v(t,ii,iib,iparm)+entfac(t)-fi_min(ii,iib,iparm))
enddo
#endif
enddo ! ii
enddo
enddo
#endif
+#ifdef DEBUG
write (iout,*) "REDUCE size",maxR,MaxT_h,nParmSet,
& maxR*MaxT_h*nParmSet
write (iout,*) "MPI_COMM_WORLD",MPI_COMM_WORLD,
& " WHAM_COMM",WHAM_COMM
+#endif
call MPI_Reduce(fi_p(1,1,1),fi(1,1,1),maxR*MaxT_h*nParmSet,
& MPI_DOUBLE_PRECISION,
& MPI_SUM,Master,WHAM_COMM,IERROR)
do iparm=1,nParmSet
do ib=1,nT_h(iparm)
do i=1,nR(ib,iparm)
- fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))
+ fi(i,ib,iparm)=-dlog(fi(i,ib,iparm))-fi_min(i,ib,iparm)
avefi=avefi+fi(i,ib,iparm)
enddo
enddo
enddo
write (iout,*) "potEmin_min",potEmin_min
#endif
-#undef DEBUG
#ifdef MPI
do t=0,tmax
projects / unres.git / commitdiff