-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_lang.inp Output file : 1L2Y_lang.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. =========================== Parameters of the MD run =========================== The units are: positions: angstrom, time: 48.9 fs velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2 energy: kcal/mol, temperature: K Number of time steps: 1000000 Initial time step of numerical integration: 0.10000 natural units 4.89000 fs Maximum acceleration threshold to reduce the time step/increase split number:********** Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000 Maximum velocity threshold to reduce velocities: 20.00000 Frequency of property output: 100 Frequency of coordinate output: 10000 Langevin dynamics calculation with direct integration of Langevin equations Temperature: 300.00000 Viscosity of the solvent: 0.89040 Radius of solvent molecule: 1.40000 Scaling factor of the friction forces: 0.01000 Eta of the solvent in natural units: 49.27846 Radii of site types and friction coefficients and std's of stochastic forces of fully exposed sites p 2.50 1.92186 4.78549 CYS 5.00 3.15382 6.13033 MET 6.20 3.74516 6.68037 PHE 6.80 4.04083 6.93906 ILE 6.20 3.74516 6.68037 LEU 6.30 3.79444 6.72418 VAL 5.80 3.54805 6.50220 TRP 7.20 4.23795 7.10629 TYR 6.90 4.09011 6.98124 ALA 4.60 2.95671 5.93567 GLY 3.80 2.56248 5.52580 THR 5.60 3.44949 6.41125 SER 4.80 3.05526 6.03378 GLN 6.10 3.69588 6.63628 ASN 5.70 3.49877 6.45688 GLU 6.10 3.69588 6.63628 ASP 5.60 3.44949 6.41125 HIS 6.20 3.74516 6.68037 ARG 6.80 4.04083 6.93906 LYS 6.30 3.79444 6.72418 PRO 5.60 3.44949 6.41125 ============================== End of MD run setup ============================= 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. ******************************************************************************** Mesoscopic molecular dynamics (MD) calculation. ******************************************************************************** Calling chainbuild ====================MD calculation start==================== Initial velocities randomly generated Initial velocities 0 0.14116 0.06019 0.00651 0.00000 0.00000 0.00000 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 2 -0.17175 -0.01249 -0.15331 -0.02090 -0.05792 -0.09881 3 0.15276 0.01076 0.15619 -0.00869 -0.01649 0.14952 4 0.09714 0.21962 -0.00076 -0.13161 0.00105 -0.13191 5 -0.28995 -0.28661 -0.04399 -0.20794 -0.09712 0.06109 6 0.02606 -0.09397 0.00121 0.02142 0.02371 0.06777 7 0.14043 0.10719 0.11062 0.03017 0.12211 0.14888 8 -0.15894 0.05289 -0.04945 -0.08870 -0.06076 0.05527 9 0.00083 -0.06721 -0.12843 0.11538 -0.05179 -0.14286 10 0.29223 -0.07835 0.13064 0.07317 0.00083 0.11341 11 -0.41159 0.15104 -0.01780 0.00000 0.00000 0.00000 12 0.28145 -0.01326 0.08243 0.00000 0.00000 0.00000 13 -0.33623 0.09347 -0.10808 -0.02992 0.03048 -0.13246 14 0.40983 0.00917 -0.03051 0.24109 -0.19177 -0.02812 15 -0.14238 -0.04269 0.11329 -0.06397 -0.14551 -0.10490 16 -0.11159 -0.01629 0.01549 0.00000 0.00000 0.00000 17 0.08712 -0.04737 0.04618 0.02491 -0.13909 -0.04091 18 -0.17195 -0.14441 -0.13341 0.13324 -0.01700 -0.06373 19 0.13399 0.09745 -0.00585 0.01171 0.10181 -0.02391 20 -0.08296 -0.16674 0.16475 0.07397 -0.09732 -0.22217 21 0.00000 0.00000 0.00000 0.05726 0.10954 -0.06352 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 Calling the zero-angular momentum subroutine vcm right after adjustment: 1.286327366462250E-017 -2.000953681163500E-017 1.837610523517500E-017 alpha-carbon coordinates centroid coordinates X Y Z X Y Z D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ASN( 2) 3.80000 0.00000 0.00000 4.26975 0.18095 1.94388 LEU( 3) 4.77894 -3.67174 0.00000 6.31901 -4.53513 -0.24135 TYR( 4) 5.40376 -3.34701 3.73419 7.55891 -4.78495 5.87678 ILE( 5) 1.60715 -3.20688 3.81267 0.73770 -2.09486 2.96799 GLN( 6) 1.94839 -6.79081 2.59652 1.68900 -6.04496 0.62369 TRP( 7) 4.28674 -7.18710 5.56554 6.59213 -8.78349 7.43105 LEU( 8) 1.35234 -5.80840 7.54758 1.63700 -4.28385 8.42522 LYS( 9) -0.53224 -8.86183 6.29662 -0.00767 -9.23195 4.00588 ASP( 10) 2.43549 -11.11658 7.03737 3.34686 -10.96549 5.22976 GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843 GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614 PRO( 13) 6.99461 -6.28836 10.29851 6.38906 -5.04979 9.95015 SER( 14) 8.57536 -7.97729 13.31326 8.27901 -7.31582 14.40566 SER( 15) 7.65918 -11.53050 12.32568 6.66212 -11.02899 11.63788 GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581 ARG( 17) 10.03694 -14.62275 8.22286 7.70563 -13.38339 8.36325 PRO( 18) 12.21420 -12.16088 6.31531 11.83401 -13.04317 5.26692 PRO( 19) 10.48638 -8.77881 6.18806 11.54928 -8.45202 7.07436 PRO( 20) 10.10763 -7.90895 2.50840 8.73829 -7.78513 2.87126 SER( 21) 11.17729 -4.27813 2.17220 10.19436 -3.61358 2.72982 D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644 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 0.000 180.000 180.000 GLY 12 3.800 101.862 -72.814 0.000 180.000 180.000 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 0.000 180.000 180.000 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 -122.045 PRO 20 3.800 106.349 -122.306 1.422 93.777 -102.374 SER 21 3.800 106.042 -134.605 1.311 153.835 -143.303 D 22 3.800 108.718 92.113 0.000 180.000 180.000 Potential energy and its components 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) Initial: Kinetic energy 2.69321E+01 potential energy -4.38013E+01 total energy -1.68691E+01 maximum acceleration 2.54656E-01 =================================== Timing =================================== MD calculations setup: 3.90625E-03 Energy & gradient evaluation: 2.37281E+02 Stochastic MD setup: 3.90625E-03 Stochastic MD step setup: 0.00000E+00 MD steps: 2.97926E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 297.949218750000 sec