X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FMD%2Fff_1l2y_1le1%2FENE%2F1L2Y_ene.out_GB000;fp=examples%2Funres%2FMD%2Fff_1l2y_1le1%2FENE%2F1L2Y_ene.out_GB000;h=0000000000000000000000000000000000000000;hp=05139d39345200e9b672680cc59623e150c153c4;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/MD/ff_1l2y_1le1/ENE/1L2Y_ene.out_GB000 b/examples/unres/MD/ff_1l2y_1le1/ENE/1L2Y_ene.out_GB000 deleted file mode 100644 index 05139d3..0000000 --- a/examples/unres/MD/ff_1l2y_1le1/ENE/1L2Y_ene.out_GB000 +++ /dev/null @@ -1,350 +0,0 @@ --------------------------------------------------------------------------------- - FILE ASSIGNMENT --------------------------------------------------------------------------------- - Input file : 1L2Y_ene.inp - Output file : 1L2Y_ene.out_GB000 - - Sidechain potential file : ../../../PARAM/scinter_GB.parm - 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_AM1.parm - Bending parameter file : ../../../PARAM/theta_abinitio.parm - Rotamer parameter file : - ../../../PARAM/rotamers_AM1_aura.10022007.parm - Threading database : ../../../PARAM/patterns.cart --------------------------------------------------------------------------------- -******************************************************************************** -United-residue force field calculation - parallel job. -******************************************************************************** - ### LAST MODIFIED 11/03/09 1:19PM by czarek - ++++ Compile info ++++ - Version 2.4 build 3228 - compiled Thu Sep 23 07:36:26 2010 - compiled by adam@matrix3.chem.cornell.edu - OS name: Linux - OS release: 2.6.27.25-170.2.72.fc10.x86_64 - OS version: #1 SMP Sun Jun 21 18:39:34 EDT 2009 - flags: - CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI ... - 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 ... - BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_... - LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/l... - ARCH = LINUX - PP = /lib/cpp -P - object = unres.o arcos.o cartprint.o chainbuild... - ++++ 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= -3059742 - ran_num 0.273754117333397 -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. - -Energy-term weights (unscaled): - -WSCC= 1.000000 (SC-SC) -WSCP= 1.233150 (SC-p) -WELEC= 0.844760 (p-p electr) -WVDWPP= 0.231730 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 0.629540 (bending) -WSCLOC= 0.105540 (SC local) -WTOR= 1.843160 (torsional) -WTORD= 1.265710 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.373570 (multi-body 3-rd order) -WCORR4= 0.192120 (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= 1.403230 (turns, 3rd order) -WTURN4= 0.646730 (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= 1.000000 (SC-SC) -WSCP= 1.233150 (SC-p) -WELEC= 0.844760 (p-p electr) -WVDWPP= 0.231730 (p-p VDW) -WBOND= 1.000000 (stretching) -WANG= 0.629540 (bending) -WSCLOC= 0.105540 (SC local) -WTOR= 1.843160 (torsional) -WTORD= 1.265710 (double torsional) -WSTRAIN= 1.000000 (SS bridges & dist. cnstr.) -WEL_LOC= 0.373570 (multi-body 3-rd order) -WCORR4= 0.192120 (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= 1.403230 (turns, 3rd order) -WTURN4= 0.646730 (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 - Processor 0 CG group 0 absolute rank 0 nhpb - 0 link_start= 1 link_end 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 2.008 102.356 -82.317 -LEU 3 3.800 104.929 0.000 1.782 120.092 -56.685 -TYR 4 3.800 87.695 -100.430 3.362 152.364 85.090 -ILE 5 3.800 81.904 72.426 1.645 134.976 -88.666 -GLN 6 3.800 82.466 66.026 2.125 122.343 -140.945 -TRP 7 3.800 84.466 51.434 3.368 152.178 38.024 -LEU 8 3.800 83.945 53.508 1.782 159.052 179.471 -LYS 9 3.800 85.396 60.569 2.379 100.558 -73.090 -ASP 10 3.800 91.449 44.177 2.030 139.961 -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 1.422 117.453 -133.163 -SER 14 3.800 94.363 -75.894 1.311 137.025 -106.659 -SER 15 3.800 96.264 67.358 1.311 146.290 -130.305 -GLY 16 3.800 138.119 129.701 0.000 0.000 0.000 -ARG 17 3.800 96.299 -95.571 2.644 93.901 -102.747 -PRO 18 3.800 129.702 63.972 1.422 101.025 -111.641 -PRO 19 3.800 109.445 -74.504 1.422 113.043 -122.044 -PRO 20 3.800 106.349 -122.306 1.422 93.778 -102.374 -SER 21 3.800 106.042 -134.605 1.311 153.835 -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. - -******************************************************************************** - - Time for energy evaluation 3.906250000000000E-003 - -Virtual-chain energies: - -EVDW= -4.743995E+01 WEIGHT= 1.000000D+00 (SC-SC) -EVDW2= 5.228224E+01 WEIGHT= 1.233150D+00 (SC-p) -EES= -1.132072E+02 WEIGHT= 8.447600D-01 (p-p) -EVDWPP= 2.375178E+01 WEIGHT= 2.317300D-01 (p-p VDW) -ESTR= 8.998619E+00 WEIGHT= 1.000000D+00 (stretching) -EBE= -1.256949E+01 WEIGHT= 6.295400D-01 (bending) -ESC= 5.871725E+01 WEIGHT= 1.055400D-01 (SC local) -ETORS= 8.243370E+00 WEIGHT= 1.843160D+00 (torsional) -ETORSD= 2.390466E+00 WEIGHT= 1.265710D+00 (double torsional) -EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) -ECORR4= -8.338619E+01 WEIGHT= 1.921200D-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= 3.735700D-01 (electrostatic-local) -ETURN3= 1.901845E+01 WEIGHT= 1.403230D+00 (turns, 3rd order) -ETURN4= -7.304754E+00 WEIGHT= 6.467300D-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= -4.380127E+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 -RMS deviation from the reference structure: 2.259 - % of native contacts: 78.571 - % of nonnative contacts: 50.000 - contact order: 0.372 -CG processor 0 is finishing work. - Total wall clock time 3.125000000000000E-002 sec