AMBER Archive (2007)

Subject: AMBER: gb minimization using nab

From: Guillaume Renvez (grenvez_at_laas.fr)
Date: Tue Nov 13 2007 - 05:06:13 CST


Hi amber users,
I'm using the newton and nmode functions of NAB to perform a
Newton-Raphson minimization followed by a vibrational frequencies
calculation in implicit solvation. When I use the option gb=1, I've
found correct GB energy compared with what I've obtained using the
Sander module of Amber 8. But when I switch to gb=2, I've got a GB
energy really much lower, which gives rise to incorrect frequencies (a
lot of them are negative then).
I've attached the input (.nab) file and the output file as well.
Does anyone know how to solve this problem?
Thanks

Guillaume

molecule m;
float x[321], grad[321], hess[103041], mass[107], fret;

m = getpdb_prm( "pept_mod_gb_min.pdb", "leaprc.ff99", "", 0 );
mm_options( "cut=12, rgbmax=12, gb=2, scnb=2.0, scee=1.2" );
mme_init( m, NULL, "::Z", x, NULL);
setxyz_from_mol( m, NULL, x );

mm_options( "ntpr=1" );
newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 6 );

nmode( x, 321, mme2, 0 );


Running: /local/users/grenvez/nab-5.1.2/bin/teLeap -s -f leap.in -I/local/users/grenvez/nab-5.1.2/leap/cmd -I/local/users/grenvez/nab-5.1.2/leap/parm -I/local/users/grenvez/nab-5.1.2/leap/prep -I/local/users/grenvez/nab-5.1.2/leap/lib > tleap.out
Reading parm file (tprmtop)
title:
                                                                                
        mm_options: cut=12
        mm_options: rgbmax=12
        mm_options: gb=2
        mm_options: scnb=2.0
        mm_options: scee=1.2
        mm_options: ntpr=1
ff: 1 -600.23 77.59 -7.43 -389.70 0.00 -280.69 8.72e-01
    iter Total bad vdW elect. cons. genBorn frms
ff: 1 -3594.80 77.59 -7.43 -389.70 0.00 -3275.25 1.98e+01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 19.8215531
For alpha = 0.00000 energy = -600.2334965788
For alpha = 1.00000 energy = 148545546.5519334376
For alpha = 0.00000 energy = -600.2335023670
For alpha = 0.00000 energy = -600.2335025800
For alpha = 0.00000 energy = -600.2335025879
For alpha = 0.00000 energy = -600.2335025880
ff: 2 -600.23 77.59 -7.43 -389.70 0.00 -280.69 8.72e-01
ff: 2 -3594.83 77.59 -7.43 -389.70 0.00 -3275.29 1.98e+01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 19.8128217
For alpha = 0.00000 energy = -600.2335025880
For alpha = 1.00000 energy = 148375081.8499098718
For alpha = 0.00000 energy = -600.2335025868
ff: 3 -600.23 77.59 -7.43 -389.70 0.00 -280.69 8.72e-01
ff: 3 -3594.83 77.59 -7.43 -389.70 0.00 -3275.29 1.98e+01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 19.8127215
For alpha = 0.00000 energy = -600.2335025868
For alpha = 1.00000 energy = 148373125.6308088601
For alpha = 0.00000 energy = -600.2335025840
ff: 4 -600.23 77.59 -7.43 -389.70 0.00 -280.69 8.72e-01
ff: 4 -3594.83 77.59 -7.43 -389.70 0.00 -3275.29 1.98e+01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 19.8126213
For alpha = 0.00000 energy = -600.2335025840
For alpha = 1.00000 energy = 148371169.4302269518
For alpha = 0.00000 energy = -600.2335025796
ff: 5 -600.23 77.59 -7.43 -389.70 0.00 -280.69 8.72e-01
ff: 5 -3594.83 77.59 -7.43 -389.70 0.00 -3275.29 1.98e+01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 19.8125210
For alpha = 0.00000 energy = -600.2335025796
For alpha = 1.00000 energy = 148369213.2481663823
For alpha = 0.00000 energy = -600.2335025736
ff: 6 -600.23 77.59 -7.43 -389.70 0.00 -280.69 8.72e-01
ff: 6 -3594.83 77.59 -7.43 -389.70 0.00 -3275.29 1.98e+01
 adding 0.00000 to diagonal of the hessian
rms of search direction: 19.8124208
For alpha = 0.00000 energy = -600.2335025736
For alpha = 1.00000 energy = 148367257.0846228302
For alpha = 0.00000 energy = -600.2335025660
    iter Total bad vdW elect. cons. genBorn frms
ff: 1 -3594.83 77.59 -7.43 -389.70 0.00 -3275.29 1.98e+01
RMS gradient = 1.98123e+01

                - Thermochemistry -

Temperature: 298.150
   Pressure: 1.000
       Mass: 836.834
Principal moments of inertia in amu-A**2:
          7084.06 32416.18 37645.64
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.003 0.001 0.001
found 39 imaginary frequencies
Zero-point vibrational energy: 521.584

             freq. E Cv S
            cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: -3048.151 168.904 226.906
translational: 0.888 2.979 46.020
rotational: 0.888 2.979 41.167
vibrational: 544.903 162.947 139.720
ff energy: -3594.831
     1 -743.884
     2 -723.548
     3 -716.943
     4 -712.399
     5 -681.789
     6 -594.167
     7 -586.157
     8 -583.305
     9 -569.267
    10 -538.468
    11 -361.792
    12 -261.862
    13 -245.068
    14 -235.735
    15 -219.961
    16 -214.207
    17 -190.687
    18 -172.360
    19 -168.056
    20 -165.922
    21 -165.725
    22 -159.733
    23 -157.884
    24 -151.436
    25 -139.059
    26 -135.476
    27 -129.078
    28 -117.810
    29 -110.476
    30 -62.943
    31 -47.546
    32 -46.393
    33 -42.572
    34 -37.638
    35 -25.605
    36 -22.490
    37 -21.683
    38 -18.762
    39 -11.983
    40 -0.000
    41 0.000
    42 0.000
    43 14.973
    44 20.569
    45 27.750
    46 45.754 0.594 1.978 4.988
    47 51.173 0.595 1.976 4.767
    48 53.229 0.595 1.975 4.689
    49 65.996 0.597 1.969 4.265
    50 67.296 0.597 1.968 4.227
    51 69.370 0.598 1.967 4.167
    52 87.680 0.601 1.956 3.707
    53 89.675 0.601 1.955 3.663
    54 100.745 0.604 1.947 3.436
    55 106.608 0.605 1.943 3.326
    56 118.180 0.608 1.933 3.126
    57 118.930 0.608 1.932 3.114
    58 130.580 0.612 1.921 2.934
    59 135.379 0.613 1.917 2.865
    60 139.300 0.614 1.913 2.810
    61 143.359 0.616 1.908 2.755
    62 160.798 0.622 1.889 2.537
    63 173.604 0.626 1.874 2.393
    64 187.289 0.632 1.856 2.252
    65 191.476 0.634 1.850 2.211
    66 195.067 0.635 1.845 2.176
    67 207.833 0.641 1.827 2.060
    68 217.266 0.645 1.813 1.979
    69 223.608 0.649 1.804 1.927
    70 233.269 0.653 1.789 1.851
    71 241.139 0.658 1.776 1.792
    72 243.269 0.659 1.772 1.776
    73 258.204 0.667 1.747 1.671
    74 268.838 0.673 1.729 1.601
    75 284.742 0.683 1.700 1.503
    76 292.766 0.688 1.686 1.456
    77 302.178 0.694 1.668 1.403
    78 303.040 0.694 1.666 1.398
    79 310.877 0.699 1.651 1.356
    80 317.661 0.704 1.638 1.320
    81 320.288 0.706 1.633 1.307
    82 324.736 0.709 1.624 1.284
    83 334.158 0.715 1.606 1.238
    84 335.014 0.716 1.604 1.234
    85 339.243 0.719 1.596 1.214
    86 343.950 0.722 1.586 1.192
    87 352.630 0.729 1.568 1.153
    88 361.038 0.735 1.551 1.116
    89 363.546 0.737 1.546 1.105
    90 370.042 0.742 1.532 1.078
    91 381.523 0.751 1.508 1.031
    92 394.785 0.761 1.480 0.980
    93 399.247 0.765 1.470 0.964
    94 411.931 0.776 1.443 0.918
    95 415.250 0.778 1.435 0.907
    96 438.191 0.798 1.385 0.831
    97 445.471 0.805 1.369 0.808
    98 449.072 0.808 1.361 0.797
    99 454.112 0.812 1.350 0.782
   100 454.898 0.813 1.348 0.780
   101 459.082 0.817 1.339 0.767
   102 462.438 0.820 1.332 0.758
   103 468.182 0.825 1.319 0.741
   104 472.955 0.830 1.308 0.728
   105 473.790 0.830 1.307 0.726
   106 480.338 0.836 1.292 0.708
   107 490.777 0.846 1.269 0.680
   108 492.553 0.848 1.265 0.676
   109 496.649 0.852 1.256 0.665
   110 503.818 0.859 1.240 0.647
   111 505.981 0.861 1.235 0.642
   112 527.137 0.882 1.188 0.592
   113 531.807 0.887 1.178 0.582
   114 536.389 0.891 1.168 0.572
   115 546.843 0.902 1.145 0.550
   116 550.220 0.905 1.138 0.543
   117 555.787 0.911 1.125 0.531
   118 564.771 0.920 1.106 0.513
   119 583.568 0.940 1.065 0.478
   120 588.490 0.946 1.055 0.469
   121 591.487 0.949 1.048 0.463
   122 607.391 0.966 1.015 0.436
   123 618.996 0.979 0.990 0.417
   124 631.301 0.992 0.965 0.398
   125 634.214 0.996 0.959 0.393
   126 649.573 1.013 0.927 0.371
   127 656.482 1.021 0.913 0.361
   128 665.438 1.031 0.895 0.349
   129 683.629 1.052 0.859 0.325
   130 688.110 1.057 0.851 0.320
   131 695.978 1.067 0.835 0.310
   132 704.281 1.076 0.820 0.300
   133 720.110 1.095 0.790 0.282
   134 738.831 1.118 0.755 0.263
   135 744.486 1.124 0.745 0.257
   136 756.569 1.139 0.724 0.245
   137 793.626 1.185 0.660 0.212
   138 803.360 1.197 0.644 0.204
   139 805.609 1.200 0.640 0.202
   140 807.821 1.203 0.637 0.200
   141 812.050 1.208 0.630 0.197
   142 815.240 1.212 0.625 0.195
   143 818.980 1.217 0.619 0.192
   144 823.077 1.222 0.612 0.189
   145 828.641 1.229 0.603 0.185
   146 832.857 1.234 0.597 0.182
   147 847.897 1.253 0.574 0.171
   148 848.622 1.254 0.573 0.171
   149 851.398 1.258 0.568 0.169
   150 852.605 1.259 0.567 0.168
   151 853.398 1.260 0.565 0.167
   152 854.993 1.262 0.563 0.166
   153 859.909 1.269 0.556 0.163
   154 862.400 1.272 0.552 0.162
   155 863.284 1.273 0.551 0.161
   156 875.984 1.289 0.532 0.153
   157 894.956 1.314 0.506 0.142
   158 898.515 1.319 0.501 0.140
   159 916.271 1.342 0.477 0.130
   160 916.504 1.342 0.477 0.130
   161 922.900 1.350 0.468 0.127
   162 940.389 1.373 0.446 0.118
   163 954.145 1.392 0.429 0.112
   164 963.056 1.403 0.418 0.108
   165 996.272 1.448 0.380 0.095
   166 999.324 1.452 0.377 0.093
   167 1005.740 1.460 0.370 0.091
   168 1011.071 1.468 0.364 0.089
   169 1012.359 1.469 0.363 0.089
   170 1016.496 1.475 0.358 0.087
   171 1041.381 1.508 0.333 0.079
   172 1051.617 1.522 0.323 0.076
   173 1054.893 1.527 0.320 0.075
   174 1066.658 1.543 0.309 0.071
   175 1068.012 1.545 0.308 0.071
   176 1074.099 1.553 0.302 0.069
   177 1083.392 1.566 0.294 0.066
   178 1087.412 1.571 0.290 0.065
   179 1099.951 1.588 0.279 0.062
   180 1105.371 1.596 0.275 0.061
   181 1114.076 1.607 0.267 0.059
   182 1122.323 1.619 0.261 0.057
   183 1143.005 1.647 0.244 0.052
   184 1153.861 1.662 0.236 0.050
   185 1181.636 1.701 0.216 0.044
   186 1183.713 1.703 0.215 0.044
   187 1184.823 1.705 0.214 0.044
   188 1198.012 1.723 0.205 0.042
   189 1268.322 1.821 0.164 0.031
   190 1272.356 1.827 0.162 0.030
   191 1276.509 1.833 0.159 0.030
   192 1276.981 1.833 0.159 0.030
   193 1280.296 1.838 0.157 0.030
   194 1282.252 1.841 0.156 0.029
   195 1283.178 1.842 0.156 0.029
   196 1283.631 1.843 0.156 0.029
   197 1285.304 1.845 0.155 0.029
   198 1287.582 1.848 0.154 0.029
   199 1288.651 1.850 0.153 0.028
   200 1291.469 1.854 0.152 0.028
   201 1293.853 1.857 0.151 0.028
   202 1309.565 1.879 0.143 0.026
   203 1314.806 1.886 0.140 0.026
   204 1320.022 1.894 0.138 0.025
   205 1323.492 1.898 0.136 0.025
   206 1328.439 1.905 0.134 0.024
   207 1329.684 1.907 0.134 0.024
   208 1338.608 1.920 0.130 0.023
   209 1342.699 1.925 0.128 0.023
   210 1345.069 1.929 0.127 0.023
   211 1393.488 1.997 0.108 0.018
   212 1399.080 2.005 0.106 0.018
   213 1401.346 2.008 0.105 0.018
   214 1402.280 2.009 0.105 0.018
   215 1403.630 2.011 0.104 0.018
   216 1404.588 2.013 0.104 0.018
   217 1408.904 2.019 0.102 0.017
   218 1418.950 2.033 0.099 0.016
   219 1420.153 2.035 0.098 0.016
   220 1432.014 2.051 0.094 0.016
   221 1432.698 2.052 0.094 0.016
   222 1433.620 2.054 0.094 0.016
   223 1439.368 2.062 0.092 0.015
   224 1442.954 2.067 0.091 0.015
   225 1443.708 2.068 0.091 0.015
   226 1447.453 2.073 0.090 0.015
   227 1454.330 2.083 0.087 0.014
   228 1466.329 2.100 0.084 0.014
   229 1470.866 2.106 0.083 0.013
   230 1474.195 2.111 0.082 0.013
   231 1480.275 2.120 0.080 0.013
   232 1485.732 2.127 0.078 0.012
   233 1493.041 2.138 0.076 0.012
   234 1498.406 2.145 0.075 0.012
   235 1511.482 2.164 0.072 0.011
   236 1520.324 2.176 0.069 0.011
   237 1531.750 2.193 0.067 0.010
   238 1537.927 2.201 0.065 0.010
   239 1546.258 2.213 0.063 0.010
   240 1558.206 2.230 0.061 0.009
   241 1558.616 2.231 0.061 0.009
   242 1560.442 2.233 0.060 0.009
   243 1560.963 2.234 0.060 0.009
   244 1562.901 2.237 0.060 0.009
   245 1632.148 2.335 0.047 0.007
   246 1643.070 2.351 0.045 0.006
   247 1649.094 2.359 0.044 0.006
   248 1653.272 2.365 0.043 0.006
   249 1657.919 2.372 0.042 0.006
   250 1657.930 2.372 0.042 0.006
   251 1663.578 2.380 0.042 0.006
   252 1678.338 2.401 0.039 0.005
   253 1679.180 2.402 0.039 0.005
   254 1682.050 2.406 0.039 0.005
   255 1682.909 2.407 0.039 0.005
   256 1689.126 2.416 0.038 0.005
   257 1693.211 2.422 0.037 0.005
   258 1735.637 2.483 0.032 0.004
   259 1736.238 2.483 0.032 0.004
   260 1739.956 2.489 0.031 0.004
   261 1740.853 2.490 0.031 0.004
   262 1742.048 2.492 0.031 0.004
   263 1751.371 2.505 0.030 0.004
   264 1754.474 2.509 0.030 0.004
   265 1762.002 2.520 0.029 0.004
   266 1763.678 2.522 0.029 0.004
   267 1768.610 2.529 0.028 0.004
   268 1772.756 2.535 0.028 0.004
   269 1779.393 2.545 0.027 0.004
   270 1780.814 2.547 0.027 0.004
   271 1787.824 2.557 0.026 0.003
   272 1864.430 2.666 0.020 0.002
   273 1871.629 2.676 0.019 0.002
   274 2903.852 4.152 0.000 0.000
   275 2907.875 4.157 0.000 0.000
   276 2908.743 4.159 0.000 0.000
   277 2914.849 4.167 0.000 0.000
   278 2916.679 4.170 0.000 0.000
   279 2916.687 4.170 0.000 0.000
   280 2917.716 4.171 0.000 0.000
   281 2917.903 4.172 0.000 0.000
   282 2917.949 4.172 0.000 0.000
   283 2943.379 4.208 0.000 0.000
   284 2943.987 4.209 0.000 0.000
   285 2944.057 4.209 0.000 0.000
   286 2944.212 4.209 0.000 0.000
   287 2945.167 4.211 0.000 0.000
   288 2958.601 4.230 0.000 0.000
   289 2977.459 4.257 0.000 0.000
   290 2980.462 4.261 0.000 0.000
   291 2981.359 4.262 0.000 0.000
   292 2982.374 4.264 0.000 0.000
   293 2987.155 4.271 0.000 0.000
   294 2987.847 4.272 0.000 0.000
   295 2988.092 4.272 0.000 0.000
   296 2988.503 4.273 0.000 0.000
   297 2988.552 4.273 0.000 0.000
   298 3083.752 4.409 0.000 0.000
   299 3084.708 4.410 0.000 0.000
   300 3085.422 4.411 0.000 0.000
   301 3086.495 4.413 0.000 0.000
   302 3193.096 4.565 0.000 0.000
   303 3315.286 4.740 0.000 0.000
   304 3316.478 4.741 0.000 0.000
   305 3319.845 4.746 0.000 0.000
   306 3326.734 4.756 0.000 0.000
   307 3336.947 4.771 0.000 0.000
   308 3354.404 4.796 0.000 0.000
   309 3355.901 4.798 0.000 0.000
   310 3361.939 4.806 0.000 0.000
   311 3366.843 4.813 0.000 0.000
   312 3373.199 4.823 0.000 0.000
   313 3374.402 4.824 0.000 0.000
   314 3374.951 4.825 0.000 0.000
   315 3377.528 4.829 0.000 0.000
   316 3487.060 4.985 0.000 0.000
   317 3495.967 4.998 0.000 0.000
   318 3508.366 5.016 0.000 0.000
   319 3528.783 5.045 0.000 0.000
   320 3530.661 5.048 0.000 0.000
   321 3718.379 5.316 0.000 0.000

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