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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Received on Wed Nov 14 2007 - 06:07:42 PST
