X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=examples%2Funres%2FCSA%2FGAB%2Flocal%2Fpdb2int%2F1l2y_pdb.out_GB000;fp=examples%2Funres%2FCSA%2FGAB%2Flocal%2Fpdb2int%2F1l2y_pdb.out_GB000;h=ef1f99e19b3dd3df3b34ff10c0d0590b37698986;hp=0000000000000000000000000000000000000000;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/examples/unres/CSA/GAB/local/pdb2int/1l2y_pdb.out_GB000 b/examples/unres/CSA/GAB/local/pdb2int/1l2y_pdb.out_GB000 new file mode 100644 index 0000000..ef1f99e --- /dev/null +++ b/examples/unres/CSA/GAB/local/pdb2int/1l2y_pdb.out_GB000 @@ -0,0 +1,282 @@ +-------------------------------------------------------------------------------- + FILE ASSIGNMENT +-------------------------------------------------------------------------------- + Input file : 1l2y_pdb.inp + Output file : 1l2y_pdb.out_GB000 + + Sidechain potential file : + /users/bartek/UNRESPACK/unres/PARAM/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16- + 10-8k + SCp potential file : /users/bartek/UNRESPACK/unres/PARAM/scp.parm + Electrostatic potential file : + /users/bartek/UNRESPACK/unres/PARAM/electr_631Gdp.parm + Cumulant coefficient file : + /users/bartek/UNRESPACK/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3 + Torsional parameter file : + /users/bartek/UNRESPACK/unres/PARAM/torsion_631Gdp.parm + Double torsional parameter file : + /users/bartek/UNRESPACK/unres/PARAM/torsion_double_631Gdp.parm + SCCOR parameter file : /users/bartek/UNRESPACK/unres/PARAM/rotcorr_AM1.parm + Bond & inertia constant file : /users/bartek/UNRESPACK/unres/PARAM/bond.parm + Bending parameter file : + /users/bartek/UNRESPACK/unres/PARAM/thetaml.5parm + Rotamer parameter file : + /users/bartek/UNRESPACK/unres/PARAM/scgauss.parm + Threading database : + /users/bartek/UNRESPACK/unres/PARAM/patterns.cart +-------------------------------------------------------------------------------- +******************************************************************************** +United-residue force field calculation - parallel job. +******************************************************************************** + ### LAST MODIFIED 11/03/09 1:19PM by czarek + ++++ Compile info ++++ + Version CSA and DFA only + +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 0 +Library routine used to diagonalize matrices. + +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) +WDFA_D= 0.000000 (DFA, distance) +WDFA_T= 0.000000 (DFA, torsional) +WDFA_N= 0.000000 (DFA, number of neighbor) +WDFA_B= 0.000000 (DFA, beta formation) + +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) +WDFA_D= 0.000000 (DFA, distance) +WDFA_T= 0.000000 (DFA, torsional) +WDFA_N= 0.000000 (DFA, number of neighbor) +WDFA_B= 0.000000 (DFA, beta formation) + 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 -10.909 3.249 -2.846 + 3 5 LEU -4.923 4.002 -2.452 -4.502 6.849 -1.550 + 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797 + 5 4 ILE -5.857 -0.449 0.613 -7.910 -0.417 1.393 + 6 13 GLN -4.122 -1.167 -2.743 -5.540 -1.315 -5.233 + 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450 + 8 5 LEU -1.641 -2.932 1.963 -2.262 -1.871 4.556 + 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 +dist_dfa.dat is opened! +phi_dfa.dat is opened! +theta_dfa.dat is opened! +nei_dfa.dat is opened! +beta_dfa.dat is opened! +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: 0.337121212121212 + Shifting contacts: 2 2 + 1 TRP 7 TYR 4 + 2 LEU 8 TYR 4 + 3 LYS 9 GLN 6 + 4 GLY 12 TRP 7 + 5 GLY 12 LEU 8 + 6 SER 14 GLY 11 + 7 SER 15 ASP 10 + 8 SER 15 GLY 11 + 9 PRO 19 TRP 7 + 10 PRO 20 LEU 3 + 11 PRO 20 TYR 4 + 12 PRO 20 TRP 7 + +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 3.861 0.000 0.000 2.611 90.531 -178.452 +LEU 3 3.876 92.239 0.000 3.016 101.575 -78.530 +TYR 4 3.861 92.239 -180.000 3.330 163.195 -7.440 +ILE 5 3.871 90.357 45.849 2.196 148.228 -110.333 +GLN 6 3.846 89.090 55.194 2.869 164.593 -141.638 +TRP 7 3.867 88.657 49.396 3.617 123.650 -21.913 +LEU 8 3.859 93.032 48.298 2.869 156.202 -108.750 +LYS 9 3.882 94.826 46.843 2.997 106.974 -55.960 +ASP 10 3.861 87.966 59.623 1.991 153.447 -128.646 +GLY 11 3.891 89.908 56.679 0.000 0.000 0.000 +GLY 12 3.864 100.181 -87.304 0.000 0.000 0.000 +PRO 13 3.886 109.073 -127.499 1.402 101.771 -115.580 +SER 14 3.876 89.537 4.261 1.267 144.515 -129.218 +SER 15 3.875 91.815 66.108 1.262 161.047 -100.177 +GLY 16 3.866 101.784 70.140 0.000 0.000 0.000 +ARG 17 3.866 92.201 -108.949 3.411 139.846 -132.716 +PRO 18 3.878 133.225 103.824 1.397 115.610 -118.024 +PRO 19 3.860 121.502 -122.527 1.395 118.575 -122.417 +PRO 20 3.858 117.950 -90.285 1.396 118.959 -126.207 +SER 21 3.864 114.201 -108.328 0.708 128.925 -37.341 +D 22 3.858 114.201 180.000 0.000 0.000 0.000 + + +******************************************************************************** + Processor 0: end reading molecular data. +******************************************************************************** + + +Energy evaluation or minimization calculation. + +******************************************************************************** + + Time for energy evaluation 0.000000000000000E+000 + +Virtual-chain energies: + +EVDW= -1.313715E+01 WEIGHT= 1.352790D+00 (SC-SC) +EVDW2= 4.471415E+01 WEIGHT= 1.593040D+00 (SC-p) +EES= -9.165378E+01 WEIGHT= 7.153400D-01 (p-p) +EVDWPP= -3.362882E+01 WEIGHT= 1.137100D-01 (p-p VDW) +ESTR= 1.489925E+03 WEIGHT= 1.000000D+00 (stretching) +EBE= -3.261471E+01 WEIGHT= 1.138730D+00 (bending) +ESC= 6.169976E+01 WEIGHT= 1.625800D-01 (SC local) +ETORS= 1.479510E+01 WEIGHT= 1.985990D+00 (torsional) +ETORSD= 1.006444E+00 WEIGHT= 1.570690D+00 (double torsional) +EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.) +ECORR4= -6.528803E+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= -4.012900E+00 WEIGHT= 1.603600D-01 (electrostatic-local) +ETURN3= 1.829789E+01 WEIGHT= 1.687220D+00 (turns, 3rd order) +ETURN4= 6.580750E-01 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) +EDFAD= 0.000000E+00 (DFA distance energy) +EDFAT= 0.000000E+00 (DFA torsion energy) +EDFAN= 0.000000E+00 (DFA NCa energy) +EDFAB= 0.000000E+00 (DFA Beta energy) +ETOT= 1.480518E+03 (total) +RMS deviation from the reference structure: 0.000 + % of native contacts: 100.000 + % of nonnative contacts: 0.000 + contact order: 0.337 +CG processor 0 is finishing work. + Total wall clock time 1.12500000000000 sec