+++ /dev/null
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- FILE ASSIGNMENT
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- 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
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-********************************************************************************
-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
projects / unres.git / blobdiff