-------------------------------------------------------------------------------- FILE ASSIGNMENT -------------------------------------------------------------------------------- Input file : 1L2Y_NVE.inp Output file : 1L2Y_NVE.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 Microcanonical mode calculation ============================== 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: 7.81250E-03 Energy & gradient evaluation: 2.39664E+02 Stochastic MD setup: 0.00000E+00 Stochastic MD step setup: 0.00000E+00 MD steps: 2.60770E+02 ============================ End of MD calculation =========================== CG processor 0 is finishing work. Total wall clock time 260.796875000000 sec