1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_ene.inp
5 Output file : 1L2Y_ene.out_GB000
7 Sidechain potential file : ../../../PARAM/scinter_GB.parm
8 SCp potential file : ../../../PARAM/scp.parm
9 Electrostatic potential file : ../../../PARAM/electr_631Gdp.parm
10 Cumulant coefficient file :
11 ../../../PARAM/fourier_opt.parm.1igd_hc_iter3_3
12 Torsional parameter file : ../../../PARAM/torsion_631Gdp.parm
13 Double torsional parameter file : ../../../PARAM/torsion_double_631Gdp.parm
14 SCCOR parameter file : ../../../PARAM/rotcorr_AM1.parm
15 Bond & inertia constant file : ../../../PARAM/bond_AM1.parm
16 Bending parameter file : ../../../PARAM/theta_abinitio.parm
17 Rotamer parameter file :
18 ../../../PARAM/rotamers_AM1_aura.10022007.parm
19 Threading database : ../../../PARAM/patterns.cart
20 --------------------------------------------------------------------------------
21 ********************************************************************************
22 United-residue force field calculation - parallel job.
23 ********************************************************************************
24 ### LAST MODIFIED 11/03/09 1:19PM by czarek
25 ++++ Compile info ++++
26 Version 2.4 build 3228
27 compiled Thu Sep 23 07:36:26 2010
28 compiled by adam@matrix3.chem.cornell.edu
30 OS release: 2.6.27.25-170.2.72.fc10.x86_64
31 OS version: #1 SMP Sun Jun 21 18:39:34 EDT 2009
33 CPPFLAGS = -DPROCOR -DLINUX -DUNRES -DMP -DMPI ...
34 INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
37 FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
38 FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
39 FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
40 FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
41 BIN = ../bin/unres_Tc_procor_new_em64_nh_hremd_...
42 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf_em64/l...
45 object = unres.o arcos.o cartprint.o chainbuild...
46 ++++ End of compile info ++++
48 Potential is GB , exponents are 6 12
50 Disulfide bridge parameters:
51 S-S bridge energy: -5.50
52 d0cm: 3.78 akcm: 15.10
53 akth: 11.00 akct: 12.00
54 v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
55 MPI: node= 0 iseed= -3059742
56 ran_num 0.273754117333397
62 Time limit (min): 960.0
64 Library routine used to diagonalize matrices.
66 Energy-term weights (unscaled):
68 WSCC= 1.000000 (SC-SC)
70 WELEC= 0.844760 (p-p electr)
71 WVDWPP= 0.231730 (p-p VDW)
72 WBOND= 1.000000 (stretching)
73 WANG= 0.629540 (bending)
74 WSCLOC= 0.105540 (SC local)
75 WTOR= 1.843160 (torsional)
76 WTORD= 1.265710 (double torsional)
77 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
78 WEL_LOC= 0.373570 (multi-body 3-rd order)
79 WCORR4= 0.192120 (multi-body 4th order)
80 WCORR5= 0.000000 (multi-body 5th order)
81 WCORR6= 0.000000 (multi-body 6th order)
82 WSCCOR= 0.000000 (back-scloc correlation)
83 WTURN3= 1.403230 (turns, 3rd order)
84 WTURN4= 0.646730 (turns, 4th order)
85 WTURN6= 0.000000 (turns, 6th order)
87 Hydrogen-bonding correlation between contact pairs of peptide groups
89 Scaling factor of 1,4 SC-p interactions: 0.400
90 General scaling factor of SC-p interactions: 1.000
92 Energy-term weights (scaled):
94 WSCC= 1.000000 (SC-SC)
96 WELEC= 0.844760 (p-p electr)
97 WVDWPP= 0.231730 (p-p VDW)
98 WBOND= 1.000000 (stretching)
99 WANG= 0.629540 (bending)
100 WSCLOC= 0.105540 (SC local)
101 WTOR= 1.843160 (torsional)
102 WTORD= 1.265710 (double torsional)
103 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
104 WEL_LOC= 0.373570 (multi-body 3-rd order)
105 WCORR4= 0.192120 (multi-body 4th order)
106 WCORR5= 0.000000 (multi-body 5th order)
107 WCORR6= 0.000000 (multi-body 6th order)
108 WSCCOR= 0.000000 (back-scloc correlatkion)
109 WTURN3= 1.403230 (turns, 3rd order)
110 WTURN4= 0.646730 (turns, 4th order)
111 WTURN6= 0.000000 (turns, 6th order)
112 Reference temperature for weights calculation: 300.000000000000
113 Parameters of the SS-bond potential:
114 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
115 11.0000000000000 AKCT 12.0000000000000
116 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
118 EBR -5.50000000000000
119 PDB data will be read from file 1L2Y.pdb
121 Backbone and SC coordinates as read from the PDB
122 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
123 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
124 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
125 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
126 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
127 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
128 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
129 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
130 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
131 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
132 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
133 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
134 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
135 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
136 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
137 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
138 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
139 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
140 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
141 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
142 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
143 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
144 nsup= 20 nstart_sup= 2
168 Boundaries in phi angle sampling:
192 nsup= 20 nstart_sup= 2 nstart_seq= 2
193 NZ_START= 2 NZ_END= 21
195 Processor 0 CG group 0 absolute rank 0 nhpb
196 0 link_start= 1 link_end 0
197 Contact order: 0.308441558441558
198 Shifting contacts: 2 2
213 Initial geometry will be read in.
215 Geometry of the virtual chain.
216 Res d Theta Gamma Dsc Alpha Beta
217 D 1 0.000 0.000 0.000 0.000 0.000 0.000
218 ASN 2 3.800 0.000 0.000 2.008 102.356 -82.317
219 LEU 3 3.800 104.929 0.000 1.782 120.092 -56.685
220 TYR 4 3.800 87.695 -100.430 3.362 152.364 85.090
221 ILE 5 3.800 81.904 72.426 1.645 134.976 -88.666
222 GLN 6 3.800 82.466 66.026 2.125 122.343 -140.945
223 TRP 7 3.800 84.466 51.434 3.368 152.178 38.024
224 LEU 8 3.800 83.945 53.508 1.782 159.052 179.471
225 LYS 9 3.800 85.396 60.569 2.379 100.558 -73.090
226 ASP 10 3.800 91.449 44.177 2.030 139.961 -144.797
227 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
228 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
229 PRO 13 3.800 119.363 -61.916 1.422 117.453 -133.163
230 SER 14 3.800 94.363 -75.894 1.311 137.025 -106.659
231 SER 15 3.800 96.264 67.358 1.311 146.290 -130.305
232 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
233 ARG 17 3.800 96.299 -95.571 2.644 93.901 -102.747
234 PRO 18 3.800 129.702 63.972 1.422 101.025 -111.641
235 PRO 19 3.800 109.445 -74.504 1.422 113.043 -122.044
236 PRO 20 3.800 106.349 -122.306 1.422 93.778 -102.374
237 SER 21 3.800 106.042 -134.605 1.311 153.835 -143.303
238 D 22 3.800 108.718 92.113 0.000 0.000 0.000
241 ********************************************************************************
242 Processor 0: end reading molecular data.
243 ********************************************************************************
246 Energy evaluation or minimization calculation.
248 ********************************************************************************
250 Time for energy evaluation 3.906250000000000E-003
252 Virtual-chain energies:
254 EVDW= -4.743995E+01 WEIGHT= 1.000000D+00 (SC-SC)
255 EVDW2= 5.228224E+01 WEIGHT= 1.233150D+00 (SC-p)
256 EES= -1.132072E+02 WEIGHT= 8.447600D-01 (p-p)
257 EVDWPP= 2.375178E+01 WEIGHT= 2.317300D-01 (p-p VDW)
258 ESTR= 8.998619E+00 WEIGHT= 1.000000D+00 (stretching)
259 EBE= -1.256949E+01 WEIGHT= 6.295400D-01 (bending)
260 ESC= 5.871725E+01 WEIGHT= 1.055400D-01 (SC local)
261 ETORS= 8.243370E+00 WEIGHT= 1.843160D+00 (torsional)
262 ETORSD= 2.390466E+00 WEIGHT= 1.265710D+00 (double torsional)
263 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
264 ECORR4= -8.338619E+01 WEIGHT= 1.921200D-01 (multi-body)
265 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
266 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
267 EELLO= -5.753258E+00 WEIGHT= 3.735700D-01 (electrostatic-local)
268 ETURN3= 1.901845E+01 WEIGHT= 1.403230D+00 (turns, 3rd order)
269 ETURN4= -7.304754E+00 WEIGHT= 6.467300D-01 (turns, 4th order)
270 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
271 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
272 EDIHC= 0.000000E+00 (dihedral angle constraints)
273 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
274 UCONST= 0.000000E+00 (Constraint energy)
275 ETOT= -4.380127E+01 (total)
305 Constants of electrostatic interaction energy expression.
306 1 1 0.7659E+08 -0.1823E+05 -0.1306E+04 0.3727E+01
307 1 2 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
308 2 1 0.4245E+08 -0.9703E+04 -0.1129E+04 0.0000E+00
309 2 2 0.6367E+08 -0.1565E+05 -0.3348E+03 0.5127E+01
310 Total average electrostatic energy: -17.0351458449875
311 VDW energy between peptide-group centers: -10.2064531653452
313 Electrostatic contacts before pruning:
314 1 ASN 2 TYR 4 -1.06027
315 2 LEU 3 ILE 5 -1.59865
316 3 LEU 3 GLN 6 -0.54360
317 4 TYR 4 GLN 6 -2.10033
318 5 TYR 4 TRP 7 -0.84900
319 6 ILE 5 TRP 7 -1.85979
320 7 ILE 5 LEU 8 -0.53540
321 8 GLN 6 LEU 8 -1.48363
322 9 GLN 6 LYS 9 -0.61868
323 10 TRP 7 LYS 9 -1.55464
324 11 TRP 7 GLY 12 -0.37651
325 12 LEU 8 ASP 10 -0.61626
326 13 LEU 8 GLY 11 -0.40662
328 Electrostatic contacts after pruning:
329 1 ASN 2 TYR 4 -1.06027
330 2 LEU 3 ILE 5 -1.59865
331 3 LEU 3 GLN 6 -0.54360
332 4 TYR 4 GLN 6 -2.10033
333 5 TYR 4 TRP 7 -0.84900
334 6 ILE 5 TRP 7 -1.85979
335 7 ILE 5 LEU 8 -0.53540
336 8 GLN 6 LEU 8 -1.48363
337 9 GLN 6 LYS 9 -0.61868
338 10 TRP 7 LYS 9 -1.55464
339 11 TRP 7 GLY 12 -0.37651
340 12 LEU 8 ASP 10 -0.61626
341 13 LEU 8 GLY 11 -0.40662
345 RMS deviation from the reference structure: 2.259
346 % of native contacts: 78.571
347 % of nonnative contacts: 50.000
349 CG processor 0 is finishing work.
350 Total wall clock time 3.125000000000000E-002 sec