1 --------------------------------------------------------------------------------
3 --------------------------------------------------------------------------------
4 Input file : 1L2Y_lang.inp
5 Output file : 1L2Y_lang.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 =========================== Parameters of the MD run ===========================
69 positions: angstrom, time: 48.9 fs
70 velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
71 energy: kcal/mol, temperature: K
73 Number of time steps: 1000000
74 Initial time step of numerical integration: 0.10000 natural units
76 Maximum acceleration threshold to reduce the time step/increase split number:**********
77 Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
78 Maximum velocity threshold to reduce velocities: 20.00000
79 Frequency of property output: 100
80 Frequency of coordinate output: 10000
82 Langevin dynamics calculation with direct integration of Langevin equations
84 Temperature: 300.00000
85 Viscosity of the solvent: 0.89040
86 Radius of solvent molecule: 1.40000
87 Scaling factor of the friction forces: 0.01000
88 Eta of the solvent in natural units: 49.27846
90 Radii of site types and friction coefficients and std's of stochastic forces of fully exposed sites
92 p 2.50 1.92186 4.78549
93 CYS 5.00 3.15382 6.13033
94 MET 6.20 3.74516 6.68037
95 PHE 6.80 4.04083 6.93906
96 ILE 6.20 3.74516 6.68037
97 LEU 6.30 3.79444 6.72418
98 VAL 5.80 3.54805 6.50220
99 TRP 7.20 4.23795 7.10629
100 TYR 6.90 4.09011 6.98124
101 ALA 4.60 2.95671 5.93567
102 GLY 3.80 2.56248 5.52580
103 THR 5.60 3.44949 6.41125
104 SER 4.80 3.05526 6.03378
105 GLN 6.10 3.69588 6.63628
106 ASN 5.70 3.49877 6.45688
107 GLU 6.10 3.69588 6.63628
108 ASP 5.60 3.44949 6.41125
109 HIS 6.20 3.74516 6.68037
110 ARG 6.80 4.04083 6.93906
111 LYS 6.30 3.79444 6.72418
112 PRO 5.60 3.44949 6.41125
114 ============================== End of MD run setup =============================
117 Energy-term weights (unscaled):
119 WSCC= 1.000000 (SC-SC)
120 WSCP= 1.233150 (SC-p)
121 WELEC= 0.844760 (p-p electr)
122 WVDWPP= 0.231730 (p-p VDW)
123 WBOND= 1.000000 (stretching)
124 WANG= 0.629540 (bending)
125 WSCLOC= 0.105540 (SC local)
126 WTOR= 1.843160 (torsional)
127 WTORD= 1.265710 (double torsional)
128 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
129 WEL_LOC= 0.373570 (multi-body 3-rd order)
130 WCORR4= 0.192120 (multi-body 4th order)
131 WCORR5= 0.000000 (multi-body 5th order)
132 WCORR6= 0.000000 (multi-body 6th order)
133 WSCCOR= 0.000000 (back-scloc correlation)
134 WTURN3= 1.403230 (turns, 3rd order)
135 WTURN4= 0.646730 (turns, 4th order)
136 WTURN6= 0.000000 (turns, 6th order)
138 Hydrogen-bonding correlation between contact pairs of peptide groups
140 Scaling factor of 1,4 SC-p interactions: 0.400
141 General scaling factor of SC-p interactions: 1.000
143 Energy-term weights (scaled):
145 WSCC= 1.000000 (SC-SC)
146 WSCP= 1.233150 (SC-p)
147 WELEC= 0.844760 (p-p electr)
148 WVDWPP= 0.231730 (p-p VDW)
149 WBOND= 1.000000 (stretching)
150 WANG= 0.629540 (bending)
151 WSCLOC= 0.105540 (SC local)
152 WTOR= 1.843160 (torsional)
153 WTORD= 1.265710 (double torsional)
154 WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
155 WEL_LOC= 0.373570 (multi-body 3-rd order)
156 WCORR4= 0.192120 (multi-body 4th order)
157 WCORR5= 0.000000 (multi-body 5th order)
158 WCORR6= 0.000000 (multi-body 6th order)
159 WSCCOR= 0.000000 (back-scloc correlatkion)
160 WTURN3= 1.403230 (turns, 3rd order)
161 WTURN4= 0.646730 (turns, 4th order)
162 WTURN6= 0.000000 (turns, 6th order)
163 Reference temperature for weights calculation: 300.000000000000
164 Parameters of the SS-bond potential:
165 D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
166 11.0000000000000 AKCT 12.0000000000000
167 V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
169 EBR -5.50000000000000
170 PDB data will be read from file 1L2Y.pdb
172 Backbone and SC coordinates as read from the PDB
173 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
174 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
175 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
176 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
177 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
178 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
179 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
180 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
181 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
182 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
183 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
184 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
185 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
186 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
187 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
188 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
189 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
190 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
191 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
192 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
193 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
194 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
195 nsup= 20 nstart_sup= 2
219 Boundaries in phi angle sampling:
243 nsup= 20 nstart_sup= 2 nstart_seq= 2
244 NZ_START= 2 NZ_END= 21
246 Processor 0 CG group 0 absolute rank 0 nhpb
247 0 link_start= 1 link_end 0
248 Contact order: 0.308441558441558
249 Shifting contacts: 2 2
264 Initial geometry will be read in.
266 Geometry of the virtual chain.
267 Res d Theta Gamma Dsc Alpha Beta
268 D 1 0.000 0.000 0.000 0.000 0.000 0.000
269 ASN 2 3.800 0.000 0.000 2.008 102.356 -82.317
270 LEU 3 3.800 104.929 0.000 1.782 120.092 -56.685
271 TYR 4 3.800 87.695 -100.430 3.362 152.364 85.090
272 ILE 5 3.800 81.904 72.426 1.645 134.976 -88.666
273 GLN 6 3.800 82.466 66.026 2.125 122.343 -140.945
274 TRP 7 3.800 84.466 51.434 3.368 152.178 38.024
275 LEU 8 3.800 83.945 53.508 1.782 159.052 179.471
276 LYS 9 3.800 85.396 60.569 2.379 100.558 -73.090
277 ASP 10 3.800 91.449 44.177 2.030 139.961 -144.797
278 GLY 11 3.800 94.602 67.604 0.000 0.000 0.000
279 GLY 12 3.800 101.862 -72.814 0.000 0.000 0.000
280 PRO 13 3.800 119.363 -61.916 1.422 117.453 -133.163
281 SER 14 3.800 94.363 -75.894 1.311 137.025 -106.659
282 SER 15 3.800 96.264 67.358 1.311 146.290 -130.305
283 GLY 16 3.800 138.119 129.701 0.000 0.000 0.000
284 ARG 17 3.800 96.299 -95.571 2.644 93.901 -102.747
285 PRO 18 3.800 129.702 63.972 1.422 101.025 -111.641
286 PRO 19 3.800 109.445 -74.504 1.422 113.043 -122.044
287 PRO 20 3.800 106.349 -122.306 1.422 93.778 -102.374
288 SER 21 3.800 106.042 -134.605 1.311 153.835 -143.303
289 D 22 3.800 108.718 92.113 0.000 0.000 0.000
292 ********************************************************************************
293 Processor 0: end reading molecular data.
294 ********************************************************************************
297 Mesoscopic molecular dynamics (MD) calculation.
299 ********************************************************************************
302 ====================MD calculation start====================
303 Initial velocities randomly generated
305 0 0.14116 0.06019 0.00651 0.00000 0.00000 0.00000
306 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
307 2 -0.17175 -0.01249 -0.15331 -0.02090 -0.05792 -0.09881
308 3 0.15276 0.01076 0.15619 -0.00869 -0.01649 0.14952
309 4 0.09714 0.21962 -0.00076 -0.13161 0.00105 -0.13191
310 5 -0.28995 -0.28661 -0.04399 -0.20794 -0.09712 0.06109
311 6 0.02606 -0.09397 0.00121 0.02142 0.02371 0.06777
312 7 0.14043 0.10719 0.11062 0.03017 0.12211 0.14888
313 8 -0.15894 0.05289 -0.04945 -0.08870 -0.06076 0.05527
314 9 0.00083 -0.06721 -0.12843 0.11538 -0.05179 -0.14286
315 10 0.29223 -0.07835 0.13064 0.07317 0.00083 0.11341
316 11 -0.41159 0.15104 -0.01780 0.00000 0.00000 0.00000
317 12 0.28145 -0.01326 0.08243 0.00000 0.00000 0.00000
318 13 -0.33623 0.09347 -0.10808 -0.02992 0.03048 -0.13246
319 14 0.40983 0.00917 -0.03051 0.24109 -0.19177 -0.02812
320 15 -0.14238 -0.04269 0.11329 -0.06397 -0.14551 -0.10490
321 16 -0.11159 -0.01629 0.01549 0.00000 0.00000 0.00000
322 17 0.08712 -0.04737 0.04618 0.02491 -0.13909 -0.04091
323 18 -0.17195 -0.14441 -0.13341 0.13324 -0.01700 -0.06373
324 19 0.13399 0.09745 -0.00585 0.01171 0.10181 -0.02391
325 20 -0.08296 -0.16674 0.16475 0.07397 -0.09732 -0.22217
326 21 0.00000 0.00000 0.00000 0.05726 0.10954 -0.06352
327 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
328 Calling the zero-angular momentum subroutine
329 vcm right after adjustment:
330 1.286327366462250E-017 -2.000953681163500E-017 1.837610523517500E-017
333 alpha-carbon coordinates centroid coordinates
335 D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
336 ASN( 2) 3.80000 0.00000 0.00000 4.26975 0.18095 1.94388
337 LEU( 3) 4.77894 -3.67174 0.00000 6.31901 -4.53513 -0.24135
338 TYR( 4) 5.40376 -3.34701 3.73419 7.55891 -4.78495 5.87678
339 ILE( 5) 1.60715 -3.20688 3.81267 0.73770 -2.09486 2.96799
340 GLN( 6) 1.94839 -6.79081 2.59652 1.68900 -6.04496 0.62369
341 TRP( 7) 4.28674 -7.18710 5.56554 6.59213 -8.78349 7.43105
342 LEU( 8) 1.35234 -5.80840 7.54758 1.63700 -4.28385 8.42522
343 LYS( 9) -0.53224 -8.86183 6.29662 -0.00767 -9.23195 4.00588
344 ASP( 10) 2.43549 -11.11658 7.03737 3.34686 -10.96549 5.22976
345 GLY( 11) 2.18504 -10.72111 10.80843 2.18504 -10.72111 10.80843
346 GLY( 12) 3.43786 -7.16826 11.30614 3.43786 -7.16826 11.30614
347 PRO( 13) 6.99461 -6.28836 10.29851 6.38906 -5.04979 9.95015
348 SER( 14) 8.57536 -7.97729 13.31326 8.27901 -7.31582 14.40566
349 SER( 15) 7.65918 -11.53050 12.32568 6.66212 -11.02899 11.63788
350 GLY( 16) 9.38152 -14.89751 11.95581 9.38152 -14.89751 11.95581
351 ARG( 17) 10.03694 -14.62275 8.22286 7.70563 -13.38339 8.36325
352 PRO( 18) 12.21420 -12.16088 6.31531 11.83401 -13.04317 5.26692
353 PRO( 19) 10.48638 -8.77881 6.18806 11.54928 -8.45202 7.07436
354 PRO( 20) 10.10763 -7.90895 2.50840 8.73829 -7.78513 2.87126
355 SER( 21) 11.17729 -4.27813 2.17220 10.19436 -3.61358 2.72982
356 D ( 22) 14.88269 -4.17086 1.33644 14.88269 -4.17086 1.33644
358 Geometry of the virtual chain.
359 Res d Theta Gamma Dsc Alpha Beta
360 D 1 0.000 0.000 0.000 0.000 0.000 0.000
361 ASN 2 3.800 0.000 0.000 2.008 102.356 -82.317
362 LEU 3 3.800 104.929 0.000 1.782 120.092 -56.685
363 TYR 4 3.800 87.695 -100.430 3.362 152.364 85.090
364 ILE 5 3.800 81.904 72.426 1.645 134.976 -88.666
365 GLN 6 3.800 82.466 66.026 2.125 122.343 -140.945
366 TRP 7 3.800 84.466 51.434 3.368 152.178 38.024
367 LEU 8 3.800 83.945 53.508 1.782 159.052 179.471
368 LYS 9 3.800 85.396 60.569 2.379 100.558 -73.090
369 ASP 10 3.800 91.449 44.177 2.030 139.961 -144.797
370 GLY 11 3.800 94.602 67.604 0.000 180.000 180.000
371 GLY 12 3.800 101.862 -72.814 0.000 180.000 180.000
372 PRO 13 3.800 119.363 -61.916 1.422 117.453 -133.163
373 SER 14 3.800 94.363 -75.894 1.311 137.025 -106.659
374 SER 15 3.800 96.264 67.358 1.311 146.290 -130.305
375 GLY 16 3.800 138.119 129.701 0.000 180.000 180.000
376 ARG 17 3.800 96.299 -95.571 2.644 93.901 -102.747
377 PRO 18 3.800 129.702 63.972 1.422 101.025 -111.641
378 PRO 19 3.800 109.445 -74.504 1.422 113.043 -122.045
379 PRO 20 3.800 106.349 -122.306 1.422 93.777 -102.374
380 SER 21 3.800 106.042 -134.605 1.311 153.835 -143.303
381 D 22 3.800 108.718 92.113 0.000 180.000 180.000
382 Potential energy and its components
384 Virtual-chain energies:
386 EVDW= -4.743995E+01 WEIGHT= 1.000000D+00 (SC-SC)
387 EVDW2= 5.228224E+01 WEIGHT= 1.233150D+00 (SC-p)
388 EES= -1.132072E+02 WEIGHT= 8.447600D-01 (p-p)
389 EVDWPP= 2.375178E+01 WEIGHT= 2.317300D-01 (p-p VDW)
390 ESTR= 8.998619E+00 WEIGHT= 1.000000D+00 (stretching)
391 EBE= -1.256949E+01 WEIGHT= 6.295400D-01 (bending)
392 ESC= 5.871725E+01 WEIGHT= 1.055400D-01 (SC local)
393 ETORS= 8.243370E+00 WEIGHT= 1.843160D+00 (torsional)
394 ETORSD= 2.390466E+00 WEIGHT= 1.265710D+00 (double torsional)
395 EHBP= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
396 ECORR4= -8.338619E+01 WEIGHT= 1.921200D-01 (multi-body)
397 ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
398 ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
399 EELLO= -5.753258E+00 WEIGHT= 3.735700D-01 (electrostatic-local)
400 ETURN3= 1.901845E+01 WEIGHT= 1.403230D+00 (turns, 3rd order)
401 ETURN4= -7.304754E+00 WEIGHT= 6.467300D-01 (turns, 4th order)
402 ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
403 ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
404 EDIHC= 0.000000E+00 (dihedral angle constraints)
405 ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
406 UCONST= 0.000000E+00 (Constraint energy)
407 ETOT= -4.380127E+01 (total)
410 Kinetic energy 2.69321E+01
411 potential energy -4.38013E+01
412 total energy -1.68691E+01
414 maximum acceleration 2.54656E-01
418 =================================== Timing ===================================
420 MD calculations setup: 3.90625E-03
421 Energy & gradient evaluation: 2.37281E+02
422 Stochastic MD setup: 3.90625E-03
423 Stochastic MD step setup: 0.00000E+00
424 MD steps: 2.97926E+02
427 ============================ End of MD calculation ===========================
428 CG processor 0 is finishing work.
429 Total wall clock time 297.949218750000 sec