AMBER Archive (2008)

Subject: AMBER: relative weight of RDC constraints

From: David Witte (david.witte_at_uni-konstanz.de)
Date: Mon Dec 15 2008 - 10:21:34 CST

Dear Amber users,
I'm recently trying to use RDC constraints for a NMR structure
refinement with Amber10. I'm performing a simulated annealing
calculation with a following energy minimization. Currently, I'm using
dwt=0.01 for the simulated annealing and dwt=0.5 for the energy
minimization. If I use dwt>0.01 for simulated annealing Amber crashes.
If I use dwt=0.01 for the energy minimization Amber doesn't seem to
include the RDCs in the calculation. In this case all calculated RDCs
have a value near 0.
I'm afraid that I might overfit the RDCs with the dwt=0.01/dwt=0.5. Do
you have any suggestions how to optimize the use of RDCs in this case?
What dwt value is normally used in NMR refinement? And are there any
general suggestions for the use of RDC constraints for NMR refinement?

The RDC input file for simulated annealing:
&align
  num_datasets=1,
  ndip=70,dwt=70*0.01,
  gigj=70*-3.1631,
  dij=70*1.041,
  dcut=-1.0,freezemol=.false.,
  dataset=1
id(1)=53, jd(1)=54, dobsu(1)= -1.90, dobsl(1)= -2.40,
id(2)=122, jd(2)=123, dobsu(2)= 9.62, dobsl(2)= 8.72,
id(3)=132, jd(3)=133, dobsu(3)= 1.34, dobsl(3)= 0.54,
id(4)=147, jd(4)=148, dobsu(4)= 2.97, dobsl(4)= 2.17,
id(5)=157, jd(5)=158, dobsu(5)= 2.06, dobsl(5)= 1.06,
id(6)=168, jd(6)=169, dobsu(6)= 5.62, dobsl(6)= 4.62,

I attached the RDC part of the output-file of the energy minimization
with dwt=0.01.

With kind regards,
David Witte


  Residual dipolar splittings:

 ------------------------------------------------------------------------------
 First atom Last atom curr. value target deviation penalty distance
 ------------------------------------------------------------------------------
 N LEU 5 -- H LEU 5: -0.061 -2.150 2.089 0.025 1.041
 N ALA 9 -- H ALA 9: 0.003 9.170 -9.167 0.683 1.041
 N GLU 10 -- H GLU 10: 0.112 0.940 -0.828 0.000 1.041
 N ALA 11 -- H ALA 11: -0.084 2.570 -2.654 0.034 1.041
 N SER 12 -- H SER 12: 0.173 1.560 -1.387 0.001 1.041
 N LEU 13 -- H LEU 13: 0.011 5.120 -5.109 0.169 1.041
 N GLY 14 -- H GLY 14: -0.049 -2.860 2.811 0.037 1.041
 N TYR 15 -- H TYR 15: -0.176 12.900 -13.076 1.482 1.041
 N THR 16 -- H THR 16: 0.110 17.760 -17.650 2.873 1.041
 N ASP 17 -- H ASP 17: 0.323 11.710 -11.387 0.881 1.041
 N ALA 18 -- H ALA 18: 0.020 -8.060 8.080 0.394 1.041
 N ASP 19 -- H ASP 19: 0.361 18.000 -17.639 2.938 1.041
 N LEU 20 -- H LEU 20: 0.266 20.620 -20.354 3.746 1.041
 N GLU 21 -- H GLU 21: 0.003 -18.890 18.893 3.346 1.041
 N GLY 22 -- H GLY 22: -0.196 -12.950 12.754 1.551 1.041
 N ALA 23 -- H ALA 23: 0.389 25.760 -25.371 6.186 1.041
 N LEU 24 -- H LEU 24: 0.038 -21.990 22.028 4.592 1.041
 N ALA 25 -- H ALA 25: 0.136 -24.440 24.576 5.701 1.041
 N LYS 26 -- H LYS 26: -0.067 -17.580 17.513 2.827 1.041
 N VAL 27 -- H VAL 27: 0.136 8.090 -7.954 0.601 1.041
 N ILE 28 -- H ILE 28: 0.321 7.210 -6.889 0.259 1.041
 N VAL 29 -- H VAL 29: -0.044 1.140 -1.184 0.000 1.041
 N SER 30 -- H SER 30: -0.016 10.830 -10.846 0.989 1.041
 N VAL 31 -- H VAL 31: 0.509 29.260 -28.751 7.981 1.041
 N ASP 34 -- H ASP 34: 0.035 6.040 -6.005 0.337 1.041
 N GLY 35 -- H GLY 35: 0.373 14.970 -14.597 1.959 1.041
 N PHE 36 -- H PHE 36: 0.039 21.320 -21.281 3.993 1.041
 N GLY 37 -- H GLY 37: -0.078 6.290 -6.368 0.344 1.041
 N GLU 38 -- H GLU 38: -0.027 1.700 -1.727 0.005 1.041
 N ILE 39 -- H ILE 39: 0.129 -0.030 0.159 0.000 1.041
 N LEU 40 -- H LEU 40: 0.008 -8.570 8.578 0.544 1.041
 N ILE 41 -- H ILE 41: 0.146 19.080 -18.934 3.585 1.041
 N SER 42 -- H SER 42: -0.148 -9.080 8.932 0.480 1.041
 N ARG 43 -- H ARG 43: -0.016 15.950 -15.966 2.331 1.041
 N GLY 46 -- H GLY 46: -0.179 12.280 -12.459 1.454 1.041
 N ALA 47 -- H ALA 47: -0.072 -1.530 1.458 0.004 1.041
 N VAL 48 -- H VAL 48: 0.012 10.110 -10.098 0.774 1.041
 N ALA 49 -- H ALA 49: -0.060 -6.800 6.740 0.254 1.041
 N LYS 50 -- H LYS 50: 0.161 -3.890 4.051 0.093 1.041
 N ALA 52 -- H ALA 52: -0.154 1.100 -1.254 0.004 1.041
 N LYS 53 -- H LYS 53: -0.213 -7.870 7.657 0.457 1.041
 N SER 54 -- H SER 54: -0.092 -0.540 0.448 0.000 1.041
 N GLU 58 -- H GLU 58: -0.417 -21.890 21.473 4.315 1.041
 N ALA 59 -- H ALA 59: -0.136 -30.540 30.404 9.123 1.041
 N ILE 60 -- H ILE 60: 0.275 25.100 -24.825 5.676 1.041
 N SER 62 -- H SER 62: -0.267 3.730 -3.997 0.090 1.041
 N GLY 63 -- H GLY 63: -0.244 -10.650 10.406 0.923 1.041
 N GLU 64 -- H GLU 64: 0.271 -19.750 20.021 3.772 1.041
 N GLU 65 -- H GLU 65: 0.260 -1.640 1.900 0.029 1.041
 N VAL 66 -- H VAL 66: -0.420 -21.800 21.380 4.194 1.041
 N ILE 67 -- H ILE 67: -0.496 -27.310 26.814 6.612 1.041
 N VAL 68 -- H VAL 68: -0.137 -11.250 11.113 1.148 1.041
 N VAL 69 -- H VAL 69: 0.156 -3.520 3.676 0.061 1.041
 N GLN 70 -- H GLN 70: -0.027 0.060 -0.087 0.000 1.041
 N MET 71 -- H MET 71: -0.100 -5.450 5.350 0.226 1.041
 N GLU 72 -- H GLU 72: -0.170 -4.870 4.700 0.160 1.041
 N GLY 74 -- H GLY 74: 0.210 12.020 -11.810 1.302 1.041
 N VAL 75 -- H VAL 75: -0.118 8.920 -9.038 0.662 1.041
 N ALA 76 -- H ALA 76: -0.084 12.140 -12.224 1.129 1.041
 N MET 77 -- H MET 77: -0.152 -18.050 17.898 3.132 1.041
 N VAL 78 -- H VAL 78: -0.047 5.300 -5.347 0.235 1.041
 N ALA 79 -- H ALA 79: -0.264 -22.990 22.726 5.119 1.041
 N LYS 80 -- H LYS 80: -0.154 -14.160 14.006 1.744 1.041
 N HID 81 -- H HID 81: 0.083 9.850 -9.767 0.935 1.041
 N ASP 82 -- H ASP 82: 0.260 1.990 -1.730 0.003 1.041
 N TYR 84 -- H TYR 84: 0.142 0.700 -0.558 0.000 1.041
 N HID 85 -- H HID 85: 0.073 -0.290 0.363 0.001 1.041
 N LEU 86 -- H LEU 86: -0.140 -4.770 4.630 0.154 1.041
 N SER 87 -- H SER 87: -0.432 -4.490 4.058 0.120 1.041
 N ILE 88 -- H ILE 88: 0.084 -1.200 1.284 0.014 1.041
                                        Total align constraint: 114.79
 Diagonalize the alignment matrix:
       -2.49477 0.86372 0.42003 -0.27849
        0.06179 0.40858 -0.90712 -0.10097
        2.43298 -0.29503 -0.02658 -0.95512
 Diagonalize the moment of interia tensor:
   549688.68259 -0.78389 -0.60701 -0.13058 24.09969
  1328886.76254 -0.12705 -0.04904 0.99068 12.49004
  1351502.10987 0.60776 -0.79318 0.03867 11.98632
 ------------------------------------------------------------------------------

--------------------------------------------------------------------------------
   5. TIMINGS
--------------------------------------------------------------------------------

| Calc gb radii 56.56 (25.04% of Gen B)
| Calc gb diag 104.91 (46.44% of Gen B)
| Calc gb off-diag 64.42 (28.52% of Gen B)
| Gen Born time 225.89 (100.0% of Nonbo)
| Nonbond force 225.89 (98.20% of Force)
| Bond/Angle/Dihedral 2.78 ( 1.21% of Force)
| Other 1.36 ( 0.59% of Force)
| Force time 230.03 (100.0% of Runmd)
| Runmd Time 230.03 (99.18% of Total)
| Other 1.89 ( 0.82% of Total)
| Total time 231.93 (100.0% of ALL )

| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 12:26:31.626 on 12/05/2008
| Setup done at 12:26:31.752 on 12/05/2008
| Run done at 12:30:23.554 on 12/05/2008
| wallclock() was called 28008 times

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