Re: [AMBER] addles "old coordinate file not specified" from Jennifer Brookes on 2011-11-09 (Amber Archive Nov 2011)

From: Jennifer Brookes <j.brookes.ucl.ac.uk>
Date: Wed, 9 Nov 2011 17:49:52 -0500

Thank you Jan-Philip and Bill everyone who has helped me with this. I have
re-formatted the .pdb file that I have and everything now works. It wasn't
ArgusLab that caused the problems, it was me manually editing it and messing
about with it so much I think that upset the formatting.

I re-loaded the .pdb in ArgusLab and re-saved it, then I altered the columns
to include all the necessary columns that Jan-Philip mentioned were absent.
Now it looks like the below and I get the desired prmtop and inpcrd files
using the method I described in previous emails.

TITLE test
REMARK 4
REMARK 4 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 6 created by ArgusLab version 4.0.1
REMARK 6 http://www.arguslab.com
REMARK 6
ATOM 1 C LIG A 1 -3.803 66.924 -0.109
C
ATOM 2 C1 LIG A 1 -3.746 68.372 0.379
C
ATOM 3 C2 LIG A 1 -4.225 69.306 -0.733
C
ATOM 4 O LIG A 1 -4.734 68.839 -1.747
O
ATOM 5 O1 LIG A 1 -4.080 70.702 -0.594
O
ATOM 6 C3 LIG A 1 -3.629 71.147 -1.854
C
ATOM 7 C4 LIG A 1 -3.437 72.666 -1.816
C
ATOM 8 C5 LIG A 1 -2.990 73.410 -3.075
C
ATOM 9 C6 LIG A 1 -2.737 72.637 -4.371
C
ATOM 10 C7 LIG A 1 -2.796 74.928 -3.037
C
ATOM 11 C8 LIG A 1 -3.091 75.512 -4.420
C
ATOM 12 C9 LIG A 1 -2.898 77.031 -4.383
C
ATOM 13 C10 LIG A 1 -2.451 77.775 -5.642
C
ATOM 14 C11 LIG A 1 -2.197 77.002 -6.937
C
ATOM 15 C12 LIG A 1 -2.258 79.292 -5.606
C
ATOM 16 C13 LIG A 1 -2.552 79.878 -6.987
C
ATOM 17 C14 LIG A 1 -2.359 81.394 -6.949
C
ATOM 18 C15 LIG A 1 -1.971 82.043 -8.046
C
ATOM 19 C16 LIG A 1 -1.776 83.561 -8.009
C
ATOM 20 C17 LIG A 1 -1.715 81.270 -9.342
C
ATOM 21 C18 LIG A 1 1.964 55.707 2.226
C
ATOM 22 C19 LIG A 1 1.495 54.298 1.855
C
ATOM 23 C20 LIG A 1 1.010 53.576 3.112
C
ATOM 24 O2 LIG A 1 0.878 54.195 4.163
O
ATOM 25 O3 LIG A 1 0.713 52.198 3.065
O
ATOM 26 C21 LIG A 1 1.265 51.666 4.246
C
ATOM 27 C22 LIG A 1 1.000 50.159 4.299
C
ATOM 28 C23 LIG A 1 1.464 49.344 5.507
C
ATOM 29 C24 LIG A 1 2.191 50.034 6.662
C
ATOM 30 C25 LIG A 1 1.197 47.837 5.558
C
ATOM 31 C26 LIG A 1 1.040 47.398 7.016
C
ATOM 32 C27 LIG A 1 0.773 45.891 7.068
C
ATOM 33 C28 LIG A 1 1.238 45.076 8.276
C
ATOM 34 C29 LIG A 1 1.966 45.766 9.431
C
ATOM 35 C30 LIG A 1 0.972 43.569 8.328
C
ATOM 36 C31 LIG A 1 0.815 43.130 9.785
C
ATOM 37 C32 LIG A 1 0.549 41.624 9.836
C
ATOM 38 C33 LIG A 1 0.951 40.914 10.887
C
ATOM 39 C34 LIG A 1 0.687 39.408 10.940
C
ATOM 40 C35 LIG A 1 1.680 41.604 12.043
C
ATOM 41 C36 LIG A 1 0.504 61.025 -1.719
C
ATOM 42 C37 LIG A 1 0.514 62.370 -1.773
C
ATOM 43 C38 LIG A 1 -0.560 62.810 -1.096
C
ATOM 44 C39 LIG A 1 -0.630 60.660 -1.104
C
ATOM 45 C40 LIG A 1 -0.910 64.069 -0.804
C
ATOM 46 C41 LIG A 1 -1.956 64.499 -0.078
C
ATOM 47 C42 LIG A 1 -3.355 66.008 1.086
C
ATOM 48 C43 LIG A 1 -3.729 64.549 1.092
C
ATOM 49 N LIG A 1 -4.607 61.732 1.407
N
ATOM 50 C44 LIG A 1 -3.953 59.062 0.805
C
ATOM 51 C45 LIG A 1 -2.189 59.049 -0.266
C
ATOM 52 C46 LIG A 1 -1.077 59.415 -0.911
C
ATOM 53 N1 LIG A 1 -2.909 63.833 0.427
N
ATOM 54 N2 LIG A 1 -3.073 59.794 0.252
N
ATOM 55 C47 LIG A 1 -2.514 57.757 -0.088
C
ATOM 56 C48 LIG A 1 -1.767 56.542 -0.565
C
ATOM 57 N3 LIG A 1 -1.264 61.754 -0.663
N
ATOM 58 C49 LIG A 1 -3.647 57.765 0.619
C
ATOM 59 C50 LIG A 1 -4.352 56.527 1.098
C
ATOM 60 C51 LIG A 1 -5.305 60.741 1.789
C
ATOM 61 C52 LIG A 1 -5.019 59.470 1.505
C
ATOM 62 C53 LIG A 1 -4.792 64.094 1.769
C
ATOM 63 C54 LIG A 1 -5.857 64.772 2.619
C
ATOM 64 C55 LIG A 1 -6.747 63.602 3.094
C
ATOM 65 C56 LIG A 1 -6.152 62.522 2.555
C
ATOM 66 C57 LIG A 1 -5.082 62.807 1.838
C
ATOM 67 C58 LIG A 1 1.522 63.220 -2.495
C
ATOM 68 C59 LIG A 1 1.546 60.060 -2.212
C
ATOM 69 C60 LIG A 1 1.366 59.705 -3.683
C
ATOM 70 O4 LIG A 1 2.844 60.528 -1.995
O
ATOM 71 C61 LIG A 1 -2.101 65.973 0.214
C
ATOM 72 C62 LIG A 1 -0.900 66.601 0.929
C
ATOM 73 O5 LIG A 1 -7.742 63.642 3.776
O
ATOM 74 C63 LIG A 1 -6.326 61.202 2.546
C
ATOM 75 C64 LIG A 1 -7.398 60.445 3.243
C
ATOM 76 C65 LIG A 1 6.899 60.995 -1.795
C
ATOM 77 C66 LIG A 1 6.668 59.669 -1.904
C
ATOM 78 C67 LIG A 1 5.532 59.375 -1.252
C
ATOM 79 C68 LIG A 1 5.836 61.514 -1.156
C
ATOM 80 C69 LIG A 1 4.959 58.181 -1.051
C
ATOM 81 C70 LIG A 1 3.860 57.888 -0.337
C
ATOM 82 C71 LIG A 1 2.400 56.580 0.954
C
ATOM 83 C72 LIG A 1 2.173 58.068 0.939
C
ATOM 84 N4 LIG A 1 1.665 60.970 1.319
N
ATOM 85 C73 LIG A 1 2.716 63.531 0.824
C
ATOM 86 C74 LIG A 1 4.488 63.312 -0.245
C
ATOM 87 C75 LIG A 1 5.534 62.792 -0.901
C
ATOM 88 N5 LIG A 1 3.061 58.673 0.256
N
ATOM 89 N6 LIG A 1 3.505 62.705 0.268
N
ATOM 90 C76 LIG A 1 4.338 64.633 -0.044
C
ATOM 91 C77 LIG A 1 5.238 65.739 -0.514
C
ATOM 92 N7 LIG A 1 5.035 60.514 -0.748
N
ATOM 93 C78 LIG A 1 3.216 64.772 0.668
C
ATOM 94 C79 LIG A 1 2.698 66.087 1.177
C
ATOM 95 C80 LIG A 1 1.093 62.035 1.712
C
ATOM 96 C81 LIG A 1 1.578 63.259 1.480
C
ATOM 97 C82 LIG A 1 1.175 58.644 1.621
C
ATOM 98 C83 LIG A 1 0.034 58.079 2.454
C
ATOM 99 C84 LIG A 1 -0.727 59.344 2.911
C
ATOM 100 C85 LIG A 1 0.002 60.357 2.409
C
ATOM 101 C86 LIG A 1 1.045 59.955 1.709
C
ATOM 102 C87 LIG A 1 7.543 58.707 -2.661
C
ATOM 103 C88 LIG A 1 8.148 61.656 -2.342
C
ATOM 104 C89 LIG A 1 8.391 63.155 -2.161
C
ATOM 105 O6 LIG A 1 9.300 60.981 -1.900
O
ATOM 106 C90 LIG A 1 3.409 56.454 -0.186
C
ATOM 107 C91 LIG A 1 2.756 55.958 -1.484
C
ATOM 108 O7 LIG A 1 -1.734 59.396 3.573
O
ATOM 109 C92 LIG A 1 -0.017 61.692 2.412
C
ATOM 110 C93 LIG A 1 -1.042 62.545 3.084
C
ATOM 111 MG1 LIG A 1 -3.169 61.830 0.000
MG
ATOM 112 MG2 LIG A 1 3.169 60.710 0.000
MG
ATOM 113 H LIG A 1 -3.155 66.808 -0.986
H
ATOM 114 H1 LIG A 1 -4.832 66.669 -0.381
H
ATOM 115 H2 LIG A 1 -2.716 68.628 0.652
H
ATOM 116 H3 LIG A 1 -4.393 68.487 1.257
H
ATOM 117 H4 LIG A 1 -2.678 70.663 -2.093
H
ATOM 118 H5 LIG A 1 -4.372 70.891 -2.617
H
ATOM 119 H6 LIG A 1 -3.617 73.218 -0.888
H
ATOM 120 H7 LIG A 1 -1.821 72.045 -4.270
H
ATOM 121 H8 LIG A 1 -3.584 71.970 -4.571
H
ATOM 122 H9 LIG A 1 -2.625 73.343 -5.200
H
ATOM 123 H10 LIG A 1 -1.763 75.158 -2.757
H
ATOM 124 H11 LIG A 1 -3.479 75.365 -2.303
H
ATOM 125 H12 LIG A 1 -4.124 75.282 -4.702
H
ATOM 126 H13 LIG A 1 -2.408 75.075 -5.155
H
ATOM 127 H14 LIG A 1 -3.079 77.584 -3.455
H
ATOM 128 H15 LIG A 1 -1.282 76.410 -6.837
H
ATOM 129 H16 LIG A 1 -3.043 76.335 -7.137
H
ATOM 130 H17 LIG A 1 -2.086 77.707 -7.768
H
ATOM 131 H18 LIG A 1 -2.940 79.730 -4.870
H
ATOM 132 H19 LIG A 1 -1.223 79.524 -5.324
H
ATOM 133 H20 LIG A 1 -3.584 79.647 -7.269
H
ATOM 134 H21 LIG A 1 -1.869 79.439 -7.723
H
ATOM 135 H22 LIG A 1 -2.539 81.948 -6.023
H
ATOM 136 H23 LIG A 1 -2.459 83.998 -7.273
H
ATOM 137 H24 LIG A 1 -0.743 83.791 -7.727
H
ATOM 138 H25 LIG A 1 -1.987 83.980 -8.998
H
ATOM 139 H26 LIG A 1 -0.802 80.679 -9.240
H
ATOM 140 H27 LIG A 1 -2.562 80.601 -9.540
H
ATOM 141 H28 LIG A 1 -1.605 81.975 -10.172
H
ATOM 142 H29 LIG A 1 2.784 55.642 2.949
H
ATOM 143 H30 LIG A 1 1.131 56.265 2.667
H
ATOM 144 H31 LIG A 1 2.328 53.741 1.414
H
ATOM 145 H32 LIG A 1 0.676 54.363 1.131
H
ATOM 146 H33 LIG A 1 2.345 51.847 4.259
H
ATOM 147 H34 LIG A 1 0.803 52.150 5.115
H
ATOM 148 H35 LIG A 1 0.478 49.665 3.471
H
ATOM 149 H36 LIG A 1 3.199 50.322 6.339
H
ATOM 150 H37 LIG A 1 1.636 50.927 6.963
H
ATOM 151 H38 LIG A 1 2.263 49.346 7.511
H
ATOM 152 H39 LIG A 1 2.039 47.302 5.106
H
ATOM 153 H40 LIG A 1 0.279 47.608 5.005
H
ATOM 154 H41 LIG A 1 0.199 47.933 7.469
H
ATOM 155 H42 LIG A 1 1.957 47.627 7.567
H
ATOM 156 H43 LIG A 1 0.251 45.397 6.241
H
ATOM 157 H44 LIG A 1 2.971 46.055 9.108
H
ATOM 158 H45 LIG A 1 1.410 46.659 9.731
H
ATOM 159 H46 LIG A 1 2.039 45.078 10.279
H
ATOM 160 H47 LIG A 1 0.054 43.341 7.776
H
ATOM 161 H48 LIG A 1 1.812 43.033 7.875
H
ATOM 162 H49 LIG A 1 -0.027 43.666 10.238
H
ATOM 163 H50 LIG A 1 1.731 43.360 10.338
H
ATOM 164 H51 LIG A 1 0.027 41.130 9.010
H
ATOM 165 H52 LIG A 1 -0.232 39.180 10.389
H
ATOM 166 H53 LIG A 1 1.526 38.873 10.486
H
ATOM 167 H54 LIG A 1 0.572 39.093 11.983
H
ATOM 168 H55 LIG A 1 2.687 41.893 11.720
H
ATOM 169 H56 LIG A 1 1.125 42.499 12.344
H
ATOM 170 H57 LIG A 1 1.752 40.917 12.892
H
ATOM 171 H58 LIG A 1 -0.231 64.850 -1.169
H
ATOM 172 H59 LIG A 1 -2.179 55.599 -0.149
H
ATOM 173 H60 LIG A 1 -0.694 56.574 -0.275
H
ATOM 174 H61 LIG A 1 -1.833 56.471 -1.674
H
ATOM 175 H62 LIG A 1 -0.462 58.600 -1.308
H
ATOM 176 H63 LIG A 1 -3.111 66.291 2.139
H
ATOM 177 H64 LIG A 1 -4.664 55.910 0.226
H
ATOM 178 H65 LIG A 1 -5.250 56.713 1.719
H
ATOM 179 H66 LIG A 1 -5.702 58.716 1.913
H
ATOM 180 H67 LIG A 1 -6.511 65.451 2.039
H
ATOM 181 H68 LIG A 1 -5.404 65.280 3.497
H
ATOM 182 H69 LIG A 1 1.108 64.209 -2.779
H
ATOM 183 H70 LIG A 1 1.830 62.749 -3.453
H
ATOM 184 H71 LIG A 1 2.424 63.415 -1.885
H
ATOM 185 H72 LIG A 1 1.516 59.113 -1.634
H
ATOM 186 H73 LIG A 1 0.381 59.220 -3.865
H
ATOM 187 H74 LIG A 1 2.166 59.017 -4.038
H
ATOM 188 H75 LIG A 1 1.411 60.626 -4.301
H
ATOM 189 H76 LIG A 1 -2.274 66.485 -0.763
H
ATOM 190 H77 LIG A 1 -0.001 66.613 0.278
H
ATOM 191 H78 LIG A 1 -0.650 66.042 1.859
H
ATOM 192 H79 LIG A 1 -1.111 67.657 1.209
H
ATOM 193 H80 LIG A 1 -7.638 59.480 2.751
H
ATOM 194 H81 LIG A 1 -8.327 61.050 3.277
H
ATOM 195 H82 LIG A 1 -7.051 60.249 4.279
H
ATOM 196 H83 LIG A 1 2.932 61.392 -2.346
H
ATOM 197 H84 LIG A 1 -3.662 55.928 1.731
H
ATOM 198 H85 LIG A 1 5.471 57.311 -1.485
H
ATOM 199 H86 LIG A 1 5.017 66.713 -0.026
H
ATOM 200 H87 LIG A 1 5.116 65.877 -1.612
H
ATOM 201 H88 LIG A 1 6.304 65.513 -0.305
H
ATOM 202 H89 LIG A 1 6.237 63.534 -1.272
H
ATOM 203 H90 LIG A 1 1.455 56.023 0.746
H
ATOM 204 H91 LIG A 1 2.373 66.720 0.323
H
ATOM 205 H92 LIG A 1 3.504 66.620 1.730
H
ATOM 206 H93 LIG A 1 0.998 64.093 1.892
H
ATOM 207 H94 LIG A 1 0.385 57.541 3.360
H
ATOM 208 H95 LIG A 1 -0.658 57.445 1.863
H
ATOM 209 H96 LIG A 1 7.675 59.064 -3.704
H
ATOM 210 H97 LIG A 1 7.131 57.680 -2.730
H
ATOM 211 H98 LIG A 1 8.544 58.616 -2.193
H
ATOM 212 H99 LIG A 1 8.121 61.470 -3.441
H
ATOM 213 H100 LIG A 1 7.701 63.762 -2.783
H
ATOM 214 H101 LIG A 1 9.409 63.462 -2.482
H
ATOM 215 H102 LIG A 1 8.314 63.466 -1.100
H
ATOM 216 H103 LIG A 1 4.262 55.788 0.094
H
ATOM 217 H104 LIG A 1 3.481 55.957 -2.329
H
ATOM 218 H105 LIG A 1 1.899 56.602 -1.779
H
ATOM 219 H106 LIG A 1 2.379 54.917 -1.365
H
ATOM 220 H107 LIG A 1 -0.983 62.392 4.182
H
ATOM 221 H108 LIG A 1 -2.054 62.234 2.747
H
ATOM 222 H109 LIG A 1 -0.936 63.628 2.866
H
ATOM 223 H110 LIG A 1 10.049 61.415 -2.275
H
ATOM 224 H111 LIG A 1 1.861 66.002 1.898
H
TER
ATOM 225 C LIG A 2 10.201 66.243 -0.109
C
ATOM 226 C1 LIG A 2 10.558 67.647 0.379
C
ATOM 227 C2 LIG A 2 10.284 68.660 -0.733
C
ATOM 228 O LIG A 2 9.689 68.309 -1.747
O
ATOM 229 O1 LIG A 2 10.716 69.995 -0.594
O
ATOM 230 C3 LIG A 2 11.249 70.337 -1.854
C
ATOM 231 C4 LIG A 2 11.753 71.782 -1.816
C
ATOM 232 C5 LIG A 2 12.345 72.417 -3.075
C
ATOM 233 C6 LIG A 2 12.432 71.608 -4.371
C
ATOM 234 C7 LIG A 2 12.851 73.861 -3.037
C
ATOM 235 C8 LIG A 2 12.683 74.494 -4.420
C
ATOM 236 C9 LIG A 2 13.188 75.939 -4.383
C
ATOM 237 C10 LIG A 2 13.780 76.574 -5.642
C
ATOM 238 C11 LIG A 2 13.868 75.765 -6.937
C
ATOM 239 C12 LIG A 2 14.284 78.017 -5.606
C
ATOM 240 C13 LIG A 2 14.119 78.651 -6.987
C
ATOM 241 C14 LIG A 2 14.623 80.094 -6.949
C
ATOM 242 C15 LIG A 2 15.137 80.648 -8.046
C
ATOM 243 C16 LIG A 2 15.644 82.092 -8.009
C
ATOM 244 C17 LIG A 2 15.227 79.839 -9.342
C
ATOM 245 C18 LIG A 2 13.508 54.073 2.226
C
ATOM 246 C19 LIG A 2 12.756 52.792 1.855
C
ATOM 247 C20 LIG A 2 12.132 52.187 3.112
C
ATOM 248 O2 LIG A 2 12.131 52.820 4.163
O
ATOM 249 O3 LIG A 2 11.554 50.901 3.065
O
ATOM 250 C21 LIG A 2 11.984 50.266 4.246
C
ATOM 251 C22 LIG A 2 11.411 48.848 4.299
C
ATOM 252 C23 LIG A 2 11.695 47.954 5.507
C
ATOM 253 C24 LIG A 2 12.550 48.478 6.662
C
ATOM 254 C25 LIG A 2 11.121 46.536 5.558
C
ATOM 255 C26 LIG A 2 10.876 46.139 7.016
C
ATOM 256 C27 LIG A 2 10.301 44.721 7.068
C
ATOM 257 C28 LIG A 2 10.587 43.827 8.276
C
ATOM 258 C29 LIG A 2 11.442 44.350 9.431
C
ATOM 259 C30 LIG A 2 10.013 42.408 8.328
C
ATOM 260 C31 LIG A 2 9.768 42.012 9.785
C
ATOM 261 C32 LIG A 2 9.195 40.594 9.836
C
ATOM 262 C33 LIG A 2 9.440 39.816 10.887
C
ATOM 263 C34 LIG A 2 8.869 38.398 10.940
C
ATOM 264 C35 LIG A 2 10.297 40.339 12.043
C
ATOM 265 C36 LIG A 2 13.186 59.578 -1.719
C
ATOM 266 C37 LIG A 2 13.476 60.891 -1.773
C
ATOM 267 C38 LIG A 2 12.517 61.545 -1.096
C
ATOM 268 C39 LIG A 2 12.001 59.457 -1.104
C
ATOM 269 C40 LIG A 2 12.436 62.849 -0.804
C
ATOM 270 C41 LIG A 2 11.503 63.487 -0.078
C
ATOM 271 C42 LIG A 2 10.448 65.254 1.086
C
ATOM 272 C43 LIG A 2 9.779 63.905 1.092
C
ATOM 273 N LIG A 2 8.335 61.332 1.407
N
ATOM 274 C44 LIG A 2 8.419 58.585 0.805
C
ATOM 275 C45 LIG A 2 10.141 58.205 -0.266
C
ATOM 276 C46 LIG A 2 11.305 58.332 -0.911
C
ATOM 277 N1 LIG A 2 10.432 63.034 0.427
N
ATOM 278 N2 LIG A 2 9.432 59.118 0.252
N
ATOM 279 C47 LIG A 2 9.555 57.009 -0.088
C
ATOM 280 C48 LIG A 2 10.033 55.666 -0.565
C
ATOM 281 N3 LIG A 2 11.609 60.658 -0.663
N
ATOM 282 C49 LIG A 2 8.448 57.253 0.619
C
ATOM 283 C50 LIG A 2 7.501 56.189 1.098
C
ATOM 284 C51 LIG A 2 7.446 60.508 1.789
C
ATOM 285 C52 LIG A 2 7.461 59.206 1.505
C
ATOM 286 C53 LIG A 2 8.645 63.681 1.769
C
ATOM 287 C54 LIG A 2 7.744 64.565 2.619
C
ATOM 288 C55 LIG A 2 6.631 63.606 3.094
C
ATOM 289 C56 LIG A 2 6.988 62.426 2.555
C
ATOM 290 C57 LIG A 2 8.094 62.482 1.838
C
ATOM 291 C58 LIG A 2 14.638 61.513 -2.495
C
ATOM 292 C59 LIG A 2 14.004 58.417 -2.212
C
ATOM 293 C60 LIG A 2 13.755 58.107 -3.683
C
ATOM 294 O4 LIG A 2 15.371 58.605 -1.995
O
ATOM 295 C61 LIG A 2 11.668 64.959 0.214
C
ATOM 296 C62 LIG A 2 12.973 65.323 0.929
C
ATOM 297 O5 LIG A 2 5.666 63.852 3.776
O
ATOM 298 C63 LIG A 2 6.543 61.171 2.546
C
ATOM 299 C64 LIG A 2 5.337 60.654 3.243
C
ATOM 300 C65 LIG A 2 19.434 58.218 -1.795
C
ATOM 301 C66 LIG A 2 18.932 56.969 -1.904
C
ATOM 302 C67 LIG A 2 17.760 56.918 -1.252
C
ATOM 303 C68 LIG A 2 18.503 58.947 -1.156
C
ATOM 304 C69 LIG A 2 16.952 55.870 -1.051
C
ATOM 305 C70 LIG A 2 15.816 55.812 -0.337
C
ATOM 306 C71 LIG A 2 14.116 54.836 0.954
C
ATOM 307 C72 LIG A 2 14.203 56.339 0.939
C
ATOM 308 N4 LIG A 2 14.310 59.282 1.319
N
ATOM 309 C73 LIG A 2 15.871 61.568 0.824
C
ATOM 310 C74 LIG A 2 17.558 60.986 -0.245
C
ATOM 311 C75 LIG A 2 18.473 60.260 -0.901
C
ATOM 312 N5 LIG A 2 15.198 56.746 0.256
N
ATOM 313 N6 LIG A 2 16.471 60.596 0.268
N
ATOM 314 C76 LIG A 2 17.686 62.309 -0.044
C
ATOM 315 C77 LIG A 2 18.796 63.203 -0.514
C
ATOM 316 N7 LIG A 2 17.511 58.135 -0.748
N
ATOM 317 C78 LIG A 2 16.618 62.678 0.668
C
ATOM 318 C79 LIG A 2 16.385 64.072 1.177
C
ATOM 319 C80 LIG A 2 13.972 60.443 1.712
C
ATOM 320 C81 LIG A 2 14.701 61.539 1.480
C
ATOM 321 C82 LIG A 2 13.347 57.109 1.621
C
ATOM 322 C83 LIG A 2 12.114 56.794 2.454
C
ATOM 323 C84 LIG A 2 11.633 58.190 2.911
C
ATOM 324 C85 LIG A 2 12.556 59.029 2.409
C
ATOM 325 C86 LIG A 2 13.493 58.419 1.709
C
ATOM 326 C87 LIG A 2 19.588 55.847 -2.661
C
ATOM 327 C88 LIG A 2 20.793 58.605 -2.342
C
ATOM 328 C89 LIG A 2 21.343 60.020 -2.161
C
ATOM 329 O6 LIG A 2 21.779 57.705 -1.900
O
ATOM 330 C90 LIG A 2 15.076 54.503 -0.186
C
ATOM 331 C91 LIG A 2 14.335 54.154 -1.484
C
ATOM 332 O7 LIG A 2 10.659 58.450 3.573
O
ATOM 333 C92 LIG A 2 12.815 60.338 2.412
C
ATOM 334 C93 LIG A 2 11.990 61.386 3.084
C
ATOM 335 MG1 LIG A 2 9.761 61.129 0.000
MG
ATOM 336 MG2 LIG A 2 15.727 58.715 0.000
MG
ATOM 337 H LIG A 2 10.810 65.994 -0.986
H
ATOM 338 H1 LIG A 2 9.141 66.207 -0.381
H
ATOM 339 H2 LIG A 2 11.618 67.683 0.652
H
ATOM 340 H3 LIG A 2 9.949 67.894 1.257
H
ATOM 341 H4 LIG A 2 12.079 69.665 -2.093
H
ATOM 342 H5 LIG A 2 10.470 70.241 -2.617
H
ATOM 343 H6 LIG A 2 11.692 72.360 -0.888
H
ATOM 344 H7 LIG A 2 13.204 70.839 -4.270
H
ATOM 345 H8 LIG A 2 11.465 71.132 -4.571
H
ATOM 346 H9 LIG A 2 12.688 72.275 -5.200
H
ATOM 347 H10 LIG A 2 13.909 73.871 -2.757
H
ATOM 348 H11 LIG A 2 12.273 74.431 -2.303
H
ATOM 349 H12 LIG A 2 11.625 74.484 -4.702
H
ATOM 350 H13 LIG A 2 13.261 73.924 -5.155
H
ATOM 351 H14 LIG A 2 13.126 76.518 -3.455
H
ATOM 352 H15 LIG A 2 14.639 74.996 -6.837
H
ATOM 353 H16 LIG A 2 12.902 75.289 -7.137
H
ATOM 354 H17 LIG A 2 14.123 76.431 -7.768
H
ATOM 355 H18 LIG A 2 13.709 78.587 -4.870
H
ATOM 356 H19 LIG A 2 15.345 78.029 -5.324
H
ATOM 357 H20 LIG A 2 13.061 78.640 -7.269
H
ATOM 358 H21 LIG A 2 14.695 78.080 -7.723
H
ATOM 359 H22 LIG A 2 14.562 80.673 -6.023
H
ATOM 360 H23 LIG A 2 15.067 82.662 -7.273
H
ATOM 361 H24 LIG A 2 16.702 82.102 -7.727
H
ATOM 362 H25 LIG A 2 15.525 82.546 -8.998
H
ATOM 363 H26 LIG A 2 15.997 79.071 -9.240
H
ATOM 364 H27 LIG A 2 14.259 79.361 -9.540
H
ATOM 365 H28 LIG A 2 15.481 80.505 -10.172
H
ATOM 366 H29 LIG A 2 14.296 53.839 2.949
H
ATOM 367 H30 LIG A 2 12.809 54.792 2.667
H
ATOM 368 H31 LIG A 2 13.455 52.074 1.414
H
ATOM 369 H32 LIG A 2 11.969 53.026 1.131
H
ATOM 370 H33 LIG A 2 13.078 50.219 4.259
H
ATOM 371 H34 LIG A 2 11.633 50.836 5.115
H
ATOM 372 H35 LIG A 2 10.798 48.473 3.471
H
ATOM 373 H36 LIG A 2 13.596 48.550 6.339
H
ATOM 374 H37 LIG A 2 12.193 49.466 6.963
H
ATOM 375 H38 LIG A 2 12.477 47.790 7.511
H
ATOM 376 H39 LIG A 2 11.833 45.837 5.106
H
ATOM 377 H40 LIG A 2 10.175 46.503 5.005
H
ATOM 378 H41 LIG A 2 10.165 46.837 7.469
H
ATOM 379 H42 LIG A 2 11.820 46.172 7.567
H
ATOM 380 H43 LIG A 2 9.688 44.346 6.241
H
ATOM 381 H44 LIG A 2 12.485 44.424 9.108
H
ATOM 382 H45 LIG A 2 11.084 45.339 9.731
H
ATOM 383 H46 LIG A 2 11.370 43.662 10.279
H
ATOM 384 H47 LIG A 2 9.068 42.376 7.776
H
ATOM 385 H48 LIG A 2 10.723 41.709 7.875
H
ATOM 386 H49 LIG A 2 9.056 42.711 10.238
H
ATOM 387 H50 LIG A 2 10.712 42.046 10.338
H
ATOM 388 H51 LIG A 2 8.581 40.220 9.010
H
ATOM 389 H52 LIG A 2 7.923 38.366 10.389
H
ATOM 390 H53 LIG A 2 9.578 37.700 10.486
H
ATOM 391 H54 LIG A 2 8.691 38.114 11.983
H
ATOM 392 H55 LIG A 2 11.342 40.412 11.720
H
ATOM 393 H56 LIG A 2 9.940 41.330 12.344
H
ATOM 394 H57 LIG A 2 10.224 39.652 12.892
H
ATOM 395 H58 LIG A 2 13.263 63.471 -1.169
H
ATOM 396 H59 LIG A 2 9.434 54.829 -0.149
H
ATOM 397 H60 LIG A 2 11.089 55.474 -0.275
H
ATOM 398 H61 LIG A 2 9.953 55.610 -1.674
H
ATOM 399 H62 LIG A 2 11.737 57.407 -1.308
H
ATOM 400 H63 LIG A 2 10.746 65.480 2.139
H
ATOM 401 H64 LIG A 2 7.068 55.650 0.226
H
ATOM 402 H65 LIG A 2 6.662 56.557 1.719
H
ATOM 403 H66 LIG A 2 6.636 58.610 1.913
H
ATOM 404 H67 LIG A 2 7.246 65.365 2.039
H
ATOM 405 H68 LIG A 2 8.293 64.968 3.497
H
ATOM 406 H69 LIG A 2 14.439 62.566 -2.779
H
ATOM 407 H70 LIG A 2 14.842 60.988 -3.453
H
ATOM 408 H71 LIG A 2 15.561 61.516 -1.885
H
ATOM 409 H72 LIG A 2 13.778 57.497 -1.634
H
ATOM 410 H73 LIG A 2 12.690 57.838 -3.865
H
ATOM 411 H74 LIG A 2 14.394 57.268 -4.038
H
ATOM 412 H75 LIG A 2 13.990 58.999 -4.301
H
ATOM 413 H76 LIG A 2 11.605 65.495 -0.763
H
ATOM 414 H77 LIG A 2 13.855 65.148 0.278
H
ATOM 415 H78 LIG A 2 13.101 64.724 1.859
H
ATOM 416 H79 LIG A 2 12.986 66.400 1.209
H
ATOM 417 H80 LIG A 2 4.902 59.760 2.751
H
ATOM 418 H81 LIG A 2 4.555 61.439 3.277
H
ATOM 419 H82 LIG A 2 5.636 60.390 4.279
H
ATOM 420 H83 LIG A 2 15.637 59.432 -2.346
H
ATOM 421 H84 LIG A 2 8.052 55.459 1.731
H
ATOM 422 H85 LIG A 2 17.271 54.912 -1.485
H
ATOM 423 H86 LIG A 2 18.783 64.202 -0.026
H
ATOM 424 H87 LIG A 2 18.706 63.364 -1.612
H
ATOM 425 H88 LIG A 2 19.792 62.760 -0.305
H
ATOM 426 H89 LIG A 2 19.315 60.839 -1.272
H
ATOM 427 H90 LIG A 2 13.076 54.488 0.746
H
ATOM 428 H91 LIG A 2 16.199 64.759 0.323
H
ATOM 429 H92 LIG A 2 17.284 64.426 1.730
H
ATOM 430 H93 LIG A 2 14.307 62.475 1.892
H
ATOM 431 H94 LIG A 2 12.345 56.195 3.360
H
ATOM 432 H95 LIG A 2 11.305 56.318 1.863
H
ATOM 433 H96 LIG A 2 19.791 56.168 -3.704
H
ATOM 434 H97 LIG A 2 18.972 54.928 -2.730
H
ATOM 435 H98 LIG A 2 20.548 55.549 -2.193
H
ATOM 436 H99 LIG A 2 20.728 58.428 -3.441
H
ATOM 437 H100 LIG A 2 20.794 60.757 -2.783
H
ATOM 438 H101 LIG A 2 22.402 60.109 -2.482
H
ATOM 439 H102 LIG A 2 21.332 60.340 -1.100
H
ATOM 440 H103 LIG A 2 15.772 53.674 0.094
H
ATOM 441 H104 LIG A 2 15.043 54.002 -2.329
H
ATOM 442 H105 LIG A 2 13.630 54.962 -1.779
H
ATOM 443 H106 LIG A 2 13.749 53.214 -1.365
H
ATOM 444 H107 LIG A 2 12.016 61.224 4.182
H
ATOM 445 H108 LIG A 2 10.936 61.292 2.747
H
ATOM 446 H109 LIG A 2 12.319 62.423 2.866
H
ATOM 447 H110 LIG A 2 22.602 57.974 -2.275
H
ATOM 448 H111 LIG A 2 15.548 64.163 1.898
H

-----Original Message-----
From: Jan-Philip Gehrcke [mailto:jgehrcke.googlemail.com]
Sent: Wednesday, November 09, 2011 11:35 AM
To: AMBER Mailing List
Subject: Re: [AMBER] addles "old coordinate file not specified"

Jenny,

your PDB ATOM lines are problematic. What is this ArgusLab software? It says
its PDB output complies (ah no, "compliel") with PDB format 2.2.

This format is specified here:
http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/pdb_contents_guide2.2.pd
f

In fact, ArgusLab obviously totally screwed up doing this job. The ATOM
lines are only correct up to the atom name, i.e. up to character 16 in the
line.

The next parts are just wrong. The residue names are missing, the residue
sequence number is missing (both are essential to leap), the chain ID is
non-existing or wrong (must be 1 character long and I don't know what "LIG"
then actually is). Actually, I don't know how leap parsed the coordinates,
if it did, because even they are in the wrong place.

Leap is assigning residue number 0 for all atoms:

Created a new atom named: C81 within residue: .R< 0>

Compare these two lines from your PDB file:

ATOM 107 N LIG 1 107 -4.607 61.732 1.407
ATOM 331 N LIG 1 331 8.335 61.332 1.407

This is the same atom name "N" and no different residue sequence number
(missing), which therefore was set to 0, leading to

residue 0: duplicate [N] atoms (total 2)

You have to find a way to get proper PDB input files... :)

Jan-Philip

On 11/09/2011 05:06 PM, Jenny C Brookes wrote:
> Thanks for your reply. I've pasted in the .pdb file below (to save
> space just the .pdb for two dimers, instead of the 60). If I do:
>
> tleap -f leap.ff99SB
>> source leaprc.gaff
>> loadamberparams dimer.frcmod
>> loadoff dimer.lib
>> LIG=loadpdb 2_dimers.pdb
>
> I get the error here:
>
>
> -- residue 0: duplicate [H6] atoms (total 2)
> -- residue 0: duplicate [H60] atoms (total 2)
> -- residue 0: duplicate [H61] atoms (total 2)
> -- residue 0: duplicate [H62] atoms (total 2)
> -- residue 0: duplicate [H63] atoms (total 2)
> -- residue 0: duplicate [H64] atoms (total 2)
> -- residue 0: duplicate [H65] atoms (total 2)
> -- residue 0: duplicate [H66] atoms (total 2)
> -- residue 0: duplicate [H67] atoms (total 2)
> -- residue 0: duplicate [H68] atoms (total 2)
> -- residue 0: duplicate [H69] atoms (total 2)
> -- residue 0: duplicate [H7] atoms (total 2)
> -- residue 0: duplicate [H70] atoms (total 2)
> -- residue 0: duplicate [H71] atoms (total 2)
> -- residue 0: duplicate [H72] atoms (total 2)
> -- residue 0: duplicate [H73] atoms (total 2)
> -- residue 0: duplicate [H74] atoms (total 2)
> -- residue 0: duplicate [H75] atoms (total 2)
> -- residue 0: duplicate [H76] atoms (total 2)
> -- residue 0: duplicate [H77] atoms (total 2)
> -- residue 0: duplicate [H78] atoms (total 2)
> -- residue 0: duplicate [H79] atoms (total 2)
> -- residue 0: duplicate [H8] atoms (total 2)
> -- residue 0: duplicate [H80] atoms (total 2)
> -- residue 0: duplicate [H81] atoms (total 2)
> -- residue 0: duplicate [H82] atoms (total 2)
> -- residue 0: duplicate [H83] atoms (total 2)
> -- residue 0: duplicate [H84] atoms (total 2)
> -- residue 0: duplicate [H85] atoms (total 2)
> -- residue 0: duplicate [H86] atoms (total 2)
> -- residue 0: duplicate [H87] atoms (total 2)
> -- residue 0: duplicate [H88] atoms (total 2)
> -- residue 0: duplicate [H89] atoms (total 2)
> -- residue 0: duplicate [H9] atoms (total 2)
> -- residue 0: duplicate [H90] atoms (total 2)
> -- residue 0: duplicate [H91] atoms (total 2)
> -- residue 0: duplicate [H92] atoms (total 2)
> -- residue 0: duplicate [H93] atoms (total 2)
> -- residue 0: duplicate [H94] atoms (total 2)
> -- residue 0: duplicate [H95] atoms (total 2)
> -- residue 0: duplicate [H96] atoms (total 2)
> -- residue 0: duplicate [H97] atoms (total 2)
> -- residue 0: duplicate [H98] atoms (total 2)
> -- residue 0: duplicate [H99] atoms (total 2)
> -- residue 0: duplicate [MG1] atoms (total 2)
> -- residue 0: duplicate [MG2] atoms (total 2)
> -- residue 0: duplicate [N] atoms (total 2)
> -- residue 0: duplicate [N1] atoms (total 2)
> -- residue 0: duplicate [N2] atoms (total 2)
> -- residue 0: duplicate [N3] atoms (total 2)
> -- residue 0: duplicate [N4] atoms (total 2)
> -- residue 0: duplicate [N5] atoms (total 2)
> -- residue 0: duplicate [N6] atoms (total 2)
> -- residue 0: duplicate [N7] atoms (total 2)
> -- residue 0: duplicate [O] atoms (total 2)
> -- residue 0: duplicate [O1] atoms (total 2)
> -- residue 0: duplicate [O2] atoms (total 2)
> -- residue 0: duplicate [O3] atoms (total 2)
> -- residue 0: duplicate [O4] atoms (total 2)
> -- residue 0: duplicate [O5] atoms (total 2)
> -- residue 0: duplicate [O6] atoms (total 2)
> -- residue 0: duplicate [O7] atoms (total 2)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Unknown residue: number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: sequence: 0
> Created a new atom named: C within residue: .R< 0>
> Created a new atom named: C1 within residue: .R< 0>
> Created a new atom named: H within residue: .R< 0>
> Created a new atom named: H1 within residue: .R< 0>
> Created a new atom named: H2 within residue: .R< 0>
> Created a new atom named: H3 within residue: .R< 0>
> Created a new atom named: C2 within residue: .R< 0>
> Created a new atom named: O within residue: .R< 0>
> Created a new atom named: O1 within residue: .R< 0>
> Created a new atom named: C3 within residue: .R< 0>
> Created a new atom named: H4 within residue: .R< 0>
> Created a new atom named: H5 within residue: .R< 0>
> Created a new atom named: C4 within residue: .R< 0>
> Created a new atom named: C5 within residue: .R< 0>
> Created a new atom named: C6 within residue: .R< 0>
> Created a new atom named: C7 within residue: .R< 0>
> Created a new atom named: C8 within residue: .R< 0>
> Created a new atom named: H6 within residue: .R< 0>
> Created a new atom named: H7 within residue: .R< 0>
> Created a new atom named: H8 within residue: .R< 0>
> Created a new atom named: H9 within residue: .R< 0>
> Created a new atom named: H10 within residue: .R< 0>
> Created a new atom named: H11 within residue: .R< 0>
> Created a new atom named: H12 within residue: .R< 0>
> Created a new atom named: H13 within residue: .R< 0>
> Created a new atom named: C9 within residue: .R< 0>
> Created a new atom named: C10 within residue: .R< 0>
> Created a new atom named: H14 within residue: .R< 0>
> Created a new atom named: C11 within residue: .R< 0>
> Created a new atom named: H15 within residue: .R< 0>
> Created a new atom named: H16 within residue: .R< 0>
> Created a new atom named: H17 within residue: .R< 0>
> Created a new atom named: C12 within residue: .R< 0>
> Created a new atom named: C13 within residue: .R< 0>
> Created a new atom named: H18 within residue: .R< 0>
> Created a new atom named: H19 within residue: .R< 0>
> Created a new atom named: H20 within residue: .R< 0>
> Created a new atom named: H21 within residue: .R< 0>
> Created a new atom named: C14 within residue: .R< 0>
> Created a new atom named: C15 within residue: .R< 0>
> Created a new atom named: C16 within residue: .R< 0>
> Created a new atom named: C17 within residue: .R< 0>
> Created a new atom named: H22 within residue: .R< 0>
> Created a new atom named: H23 within residue: .R< 0>
> Created a new atom named: H24 within residue: .R< 0>
> Created a new atom named: H25 within residue: .R< 0>
> Created a new atom named: H26 within residue: .R< 0>
> Created a new atom named: H27 within residue: .R< 0>
> Created a new atom named: H28 within residue: .R< 0>
> Created a new atom named: C18 within residue: .R< 0>
> Created a new atom named: C19 within residue: .R< 0>
> Created a new atom named: H29 within residue: .R< 0>
> Created a new atom named: H30 within residue: .R< 0>
> Created a new atom named: H31 within residue: .R< 0>
> Created a new atom named: H32 within residue: .R< 0>
> Created a new atom named: C20 within residue: .R< 0>
> Created a new atom named: O2 within residue: .R< 0>
> Created a new atom named: O3 within residue: .R< 0>
> Created a new atom named: C21 within residue: .R< 0>
> Created a new atom named: H33 within residue: .R< 0>
> Created a new atom named: H34 within residue: .R< 0>
> Created a new atom named: C22 within residue: .R< 0>
> Created a new atom named: C23 within residue: .R< 0>
> Created a new atom named: C24 within residue: .R< 0>
> Created a new atom named: C25 within residue: .R< 0>
> Created a new atom named: C26 within residue: .R< 0>
> Created a new atom named: H35 within residue: .R< 0>
> Created a new atom named: H36 within residue: .R< 0>
> Created a new atom named: H37 within residue: .R< 0>
> Created a new atom named: H38 within residue: .R< 0>
> Created a new atom named: H39 within residue: .R< 0>
> Created a new atom named: H40 within residue: .R< 0>
> Created a new atom named: H41 within residue: .R< 0>
> Created a new atom named: H42 within residue: .R< 0>
> Created a new atom named: C27 within residue: .R< 0>
> Created a new atom named: C28 within residue: .R< 0>
> Created a new atom named: H43 within residue: .R< 0>
> Created a new atom named: C29 within residue: .R< 0>
> Created a new atom named: H44 within residue: .R< 0>
> Created a new atom named: H45 within residue: .R< 0>
> Created a new atom named: H46 within residue: .R< 0>
> Created a new atom named: C30 within residue: .R< 0>
> Created a new atom named: C31 within residue: .R< 0>
> Created a new atom named: H47 within residue: .R< 0>
> Created a new atom named: H48 within residue: .R< 0>
> Created a new atom named: H49 within residue: .R< 0>
> Created a new atom named: H50 within residue: .R< 0>
> Created a new atom named: C32 within residue: .R< 0>
> Created a new atom named: C33 within residue: .R< 0>
> Created a new atom named: C34 within residue: .R< 0>
> Created a new atom named: C35 within residue: .R< 0>
> Created a new atom named: H51 within residue: .R< 0>
> Created a new atom named: H52 within residue: .R< 0>
> Created a new atom named: H53 within residue: .R< 0>
> Created a new atom named: H54 within residue: .R< 0>
> Created a new atom named: H55 within residue: .R< 0>
> Created a new atom named: H56 within residue: .R< 0>
> Created a new atom named: H57 within residue: .R< 0>
> Created a new atom named: C36 within residue: .R< 0>
> Created a new atom named: C37 within residue: .R< 0>
> Created a new atom named: C38 within residue: .R< 0>
> Created a new atom named: C39 within residue: .R< 0>
> Created a new atom named: C40 within residue: .R< 0>
> Created a new atom named: C41 within residue: .R< 0>
> Created a new atom named: C42 within residue: .R< 0>
> Created a new atom named: C43 within residue: .R< 0>
> Created a new atom named: N within residue: .R< 0>
> Created a new atom named: C44 within residue: .R< 0>
> Created a new atom named: C45 within residue: .R< 0>
> Created a new atom named: C46 within residue: .R< 0>
> Created a new atom named: N1 within residue: .R< 0>
> Created a new atom named: N2 within residue: .R< 0>
> Created a new atom named: H58 within residue: .R< 0>
> Created a new atom named: C47 within residue: .R< 0>
> Created a new atom named: C48 within residue: .R< 0>
> Created a new atom named: H59 within residue: .R< 0>
> Created a new atom named: H60 within residue: .R< 0>
> Created a new atom named: H61 within residue: .R< 0>
> Created a new atom named: N3 within residue: .R< 0>
> Created a new atom named: H62 within residue: .R< 0>
> Created a new atom named: C49 within residue: .R< 0>
> Created a new atom named: C50 within residue: .R< 0>
> Created a new atom named: C51 within residue: .R< 0>
> Created a new atom named: C52 within residue: .R< 0>
> Created a new atom named: C53 within residue: .R< 0>
> Created a new atom named: C54 within residue: .R< 0>
> Created a new atom named: C55 within residue: .R< 0>
> Created a new atom named: C56 within residue: .R< 0>
> Created a new atom named: C57 within residue: .R< 0>
> Created a new atom named: C58 within residue: .R< 0>
> Created a new atom named: C59 within residue: .R< 0>
> Created a new atom named: C60 within residue: .R< 0>
> Created a new atom named: O4 within residue: .R< 0>
> Created a new atom named: C61 within residue: .R< 0>
> Created a new atom named: C62 within residue: .R< 0>
> Created a new atom named: H63 within residue: .R< 0>
> Created a new atom named: H64 within residue: .R< 0>
> Created a new atom named: H65 within residue: .R< 0>
> Created a new atom named: H66 within residue: .R< 0>
> Created a new atom named: H67 within residue: .R< 0>
> Created a new atom named: H68 within residue: .R< 0>
> Created a new atom named: H69 within residue: .R< 0>
> Created a new atom named: H70 within residue: .R< 0>
> Created a new atom named: H71 within residue: .R< 0>
> Created a new atom named: H72 within residue: .R< 0>
> Created a new atom named: H73 within residue: .R< 0>
> Created a new atom named: H74 within residue: .R< 0>
> Created a new atom named: H75 within residue: .R< 0>
> Created a new atom named: H76 within residue: .R< 0>
> Created a new atom named: H77 within residue: .R< 0>
> Created a new atom named: H78 within residue: .R< 0>
> Created a new atom named: H79 within residue: .R< 0>
> Created a new atom named: O5 within residue: .R< 0>
> Created a new atom named: C63 within residue: .R< 0>
> Created a new atom named: C64 within residue: .R< 0>
> Created a new atom named: H80 within residue: .R< 0>
> Created a new atom named: H81 within residue: .R< 0>
> Created a new atom named: H82 within residue: .R< 0>
> Created a new atom named: H83 within residue: .R< 0>
> Created a new atom named: H84 within residue: .R< 0>
> Created a new atom named: C65 within residue: .R< 0>
> Created a new atom named: C66 within residue: .R< 0>
> Created a new atom named: C67 within residue: .R< 0>
> Created a new atom named: C68 within residue: .R< 0>
> Created a new atom named: C69 within residue: .R< 0>
> Created a new atom named: C70 within residue: .R< 0>
> Created a new atom named: C71 within residue: .R< 0>
> Created a new atom named: C72 within residue: .R< 0>
> Created a new atom named: N4 within residue: .R< 0>
> Created a new atom named: C73 within residue: .R< 0>
> Created a new atom named: C74 within residue: .R< 0>
> Created a new atom named: C75 within residue: .R< 0>
> Created a new atom named: N5 within residue: .R< 0>
> Created a new atom named: N6 within residue: .R< 0>
> Created a new atom named: H85 within residue: .R< 0>
> Created a new atom named: C76 within residue: .R< 0>
> Created a new atom named: C77 within residue: .R< 0>
> Created a new atom named: H86 within residue: .R< 0>
> Created a new atom named: H87 within residue: .R< 0>
> Created a new atom named: H88 within residue: .R< 0>
> Created a new atom named: N7 within residue: .R< 0>
> Created a new atom named: H89 within residue: .R< 0>
> Created a new atom named: C78 within residue: .R< 0>
> Created a new atom named: C79 within residue: .R< 0>
> Created a new atom named: C80 within residue: .R< 0>
> Created a new atom named: C81 within residue: .R< 0>
> Created a new atom named: C82 within residue: .R< 0>
> Created a new atom named: C83 within residue: .R< 0>
> Created a new atom named: C84 within residue: .R< 0>
> Created a new atom named: C85 within residue: .R< 0>
> Created a new atom named: C86 within residue: .R< 0>
> Created a new atom named: C87 within residue: .R< 0>
> Created a new atom named: C88 within residue: .R< 0>
> Created a new atom named: C89 within residue: .R< 0>
> Created a new atom named: O6 within residue: .R< 0>
> Created a new atom named: C90 within residue: .R< 0>
> Created a new atom named: C91 within residue: .R< 0>
> Created a new atom named: H90 within residue: .R< 0>
> Created a new atom named: H91 within residue: .R< 0>
> Created a new atom named: H92 within residue: .R< 0>
> Created a new atom named: H93 within residue: .R< 0>
> Created a new atom named: H94 within residue: .R< 0>
> Created a new atom named: H95 within residue: .R< 0>
> Created a new atom named: H96 within residue: .R< 0>
> Created a new atom named: H97 within residue: .R< 0>
> Created a new atom named: H98 within residue: .R< 0>
> Created a new atom named: H99 within residue: .R< 0>
> Created a new atom named: H100 within residue: .R< 0>
> Created a new atom named: H101 within residue: .R< 0>
> Created a new atom named: H102 within residue: .R< 0>
> Created a new atom named: H103 within residue: .R< 0>
> Created a new atom named: H104 within residue: .R< 0>
> Created a new atom named: H105 within residue: .R< 0>
> Created a new atom named: H106 within residue: .R< 0>
> Created a new atom named: O7 within residue: .R< 0>
> Created a new atom named: C92 within residue: .R< 0>
> Created a new atom named: C93 within residue: .R< 0>
> Created a new atom named: H107 within residue: .R< 0>
> Created a new atom named: H108 within residue: .R< 0>
> Created a new atom named: H109 within residue: .R< 0>
> Created a new atom named: H110 within residue: .R< 0>
> Created a new atom named: H111 within residue: .R< 0>
> Created a new atom named: MG1 within residue: .R< 0>
> Created a new atom named: MG2 within residue: .R< 0>
> total atoms in file: 448
> The file contained 224 atoms not in residue templates
>
>
> and I cannot saveamberparms. The 2_dimers.pdb file I use is below:
>
>
> TITLE 2_dimers
> REMARK 4
> REMARK 4 COMPLIEL WITH FORMAT V. 2.2, 16-DEC-1996
> REMARK 6 created by ArgusLab version 4.0.1
> REMARK 6 http://www.arguslab.com
> REMARK 6
> ATOM 1 C LIG 1 1 -3.803 66.924 -0.109
> ATOM 2 C1 LIG 1 2 -3.746 68.372 0.379
> ATOM 3 H LIG 1 3 -3.155 66.808 -0.986
> ATOM 4 H1 LIG 1 4 -4.832 66.669 -0.381
> ATOM 5 H2 LIG 1 5 -2.716 68.628 0.652
> ATOM 6 H3 LIG 1 6 -4.393 68.487 1.257
> ATOM 7 C2 LIG 1 7 -4.225 69.306 -0.733
> ATOM 8 O LIG 1 8 -4.734 68.839 -1.747
> ATOM 9 O1 LIG 1 9 -4.080 70.702 -0.594
> ATOM 10 C3 LIG 1 10 -3.629 71.147 -1.854
> ATOM 11 H4 LIG 1 11 -2.678 70.663 -2.093
> ATOM 12 H5 LIG 1 12 -4.372 70.891 -2.617
> ATOM 13 C4 LIG 1 13 -3.437 72.666 -1.816
> ATOM 14 C5 LIG 1 14 -2.990 73.410 -3.075
> ATOM 15 C6 LIG 1 15 -2.737 72.637 -4.371
> ATOM 16 C7 LIG 1 16 -2.796 74.928 -3.037
> ATOM 17 C8 LIG 1 17 -3.091 75.512 -4.420
> ATOM 18 H6 LIG 1 18 -3.617 73.218 -0.888
> ATOM 19 H7 LIG 1 19 -1.821 72.045 -4.270
> ATOM 20 H8 LIG 1 20 -3.584 71.970 -4.571
> ATOM 21 H9 LIG 1 21 -2.625 73.343 -5.200
> ATOM 22 H10 LIG 1 22 -1.763 75.158 -2.757
> ATOM 23 H11 LIG 1 23 -3.479 75.365 -2.303
> ATOM 24 H12 LIG 1 24 -4.124 75.282 -4.702
> ATOM 25 H13 LIG 1 25 -2.408 75.075 -5.155
> ATOM 26 C9 LIG 1 26 -2.898 77.031 -4.383
> ATOM 27 C10 LIG 1 27 -2.451 77.775 -5.642
> ATOM 28 H14 LIG 1 28 -3.079 77.584 -3.455
> ATOM 29 C11 LIG 1 29 -2.197 77.002 -6.937
> ATOM 30 H15 LIG 1 30 -1.282 76.410 -6.837
> ATOM 31 H16 LIG 1 31 -3.043 76.335 -7.137
> ATOM 32 H17 LIG 1 32 -2.086 77.707 -7.768
> ATOM 33 C12 LIG 1 33 -2.258 79.292 -5.606
> ATOM 34 C13 LIG 1 34 -2.552 79.878 -6.987
> ATOM 35 H18 LIG 1 35 -2.940 79.730 -4.870
> ATOM 36 H19 LIG 1 36 -1.223 79.524 -5.324
> ATOM 37 H20 LIG 1 37 -3.584 79.647 -7.269
> ATOM 38 H21 LIG 1 38 -1.869 79.439 -7.723
> ATOM 39 C14 LIG 1 39 -2.359 81.394 -6.949
> ATOM 40 C15 LIG 1 40 -1.971 82.043 -8.046
> ATOM 41 C16 LIG 1 41 -1.776 83.561 -8.009
> ATOM 42 C17 LIG 1 42 -1.715 81.270 -9.342
> ATOM 43 H22 LIG 1 43 -2.539 81.948 -6.023
> ATOM 44 H23 LIG 1 44 -2.459 83.998 -7.273
> ATOM 45 H24 LIG 1 45 -0.743 83.791 -7.727
> ATOM 46 H25 LIG 1 46 -1.987 83.980 -8.998
> ATOM 47 H26 LIG 1 47 -0.802 80.679 -9.240
> ATOM 48 H27 LIG 1 48 -2.562 80.601 -9.540
> ATOM 49 H28 LIG 1 49 -1.605 81.975 -10.172
> ATOM 50 C18 LIG 1 50 1.964 55.707 2.226
> ATOM 51 C19 LIG 1 51 1.495 54.298 1.855
> ATOM 52 H29 LIG 1 52 2.784 55.642 2.949
> ATOM 53 H30 LIG 1 53 1.131 56.265 2.667
> ATOM 54 H31 LIG 1 54 2.328 53.741 1.414
> ATOM 55 H32 LIG 1 55 0.676 54.363 1.131
> ATOM 56 C20 LIG 1 56 1.010 53.576 3.112
> ATOM 57 O2 LIG 1 57 0.878 54.195 4.163
> ATOM 58 O3 LIG 1 58 0.713 52.198 3.065
> ATOM 59 C21 LIG 1 59 1.265 51.666 4.246
> ATOM 60 H33 LIG 1 60 2.345 51.847 4.259
> ATOM 61 H34 LIG 1 61 0.803 52.150 5.115
> ATOM 62 C22 LIG 1 62 1.000 50.159 4.299
> ATOM 63 C23 LIG 1 63 1.464 49.344 5.507
> ATOM 64 C24 LIG 1 64 2.191 50.034 6.662
> ATOM 65 C25 LIG 1 65 1.197 47.837 5.558
> ATOM 66 C26 LIG 1 66 1.040 47.398 7.016
> ATOM 67 H35 LIG 1 67 0.478 49.665 3.471
> ATOM 68 H36 LIG 1 68 3.199 50.322 6.339
> ATOM 69 H37 LIG 1 69 1.636 50.927 6.963
> ATOM 70 H38 LIG 1 70 2.263 49.346 7.511
> ATOM 71 H39 LIG 1 71 2.039 47.302 5.106
> ATOM 72 H40 LIG 1 72 0.279 47.608 5.005
> ATOM 73 H41 LIG 1 73 0.199 47.933 7.469
> ATOM 74 H42 LIG 1 74 1.957 47.627 7.567
> ATOM 75 C27 LIG 1 75 0.773 45.891 7.068
> ATOM 76 C28 LIG 1 76 1.238 45.076 8.276
> ATOM 77 H43 LIG 1 77 0.251 45.397 6.241
> ATOM 78 C29 LIG 1 78 1.966 45.766 9.431
> ATOM 79 H44 LIG 1 79 2.971 46.055 9.108
> ATOM 80 H45 LIG 1 80 1.410 46.659 9.731
> ATOM 81 H46 LIG 1 81 2.039 45.078 10.279
> ATOM 82 C30 LIG 1 82 0.972 43.569 8.328
> ATOM 83 C31 LIG 1 83 0.815 43.130 9.785
> ATOM 84 H47 LIG 1 84 0.054 43.341 7.776
> ATOM 85 H48 LIG 1 85 1.812 43.033 7.875
> ATOM 86 H49 LIG 1 86 -0.027 43.666 10.238
> ATOM 87 H50 LIG 1 87 1.731 43.360 10.338
> ATOM 88 C32 LIG 1 88 0.549 41.624 9.836
> ATOM 89 C33 LIG 1 89 0.951 40.914 10.887
> ATOM 90 C34 LIG 1 90 0.687 39.408 10.940
> ATOM 91 C35 LIG 1 91 1.680 41.604 12.043
> ATOM 92 H51 LIG 1 92 0.027 41.130 9.010
> ATOM 93 H52 LIG 1 93 -0.232 39.180 10.389
> ATOM 94 H53 LIG 1 94 1.526 38.873 10.486
> ATOM 95 H54 LIG 1 95 0.572 39.093 11.983
> ATOM 96 H55 LIG 1 96 2.687 41.893 11.720
> ATOM 97 H56 LIG 1 97 1.125 42.499 12.344
> ATOM 98 H57 LIG 1 98 1.752 40.917 12.892
> ATOM 99 C36 LIG 1 99 0.504 61.025 -1.719
> ATOM 100 C37 LIG 1 100 0.514 62.370 -1.773
> ATOM 101 C38 LIG 1 101 -0.560 62.810 -1.096
> ATOM 102 C39 LIG 1 102 -0.630 60.660 -1.104
> ATOM 103 C40 LIG 1 103 -0.910 64.069 -0.804
> ATOM 104 C41 LIG 1 104 -1.956 64.499 -0.078
> ATOM 105 C42 LIG 1 105 -3.355 66.008 1.086
> ATOM 106 C43 LIG 1 106 -3.729 64.549 1.092
> ATOM 107 N LIG 1 107 -4.607 61.732 1.407
> ATOM 108 C44 LIG 1 108 -3.953 59.062 0.805
> ATOM 109 C45 LIG 1 109 -2.189 59.049 -0.266
> ATOM 110 C46 LIG 1 110 -1.077 59.415 -0.911
> ATOM 111 N1 LIG 1 111 -2.909 63.833 0.427
> ATOM 112 N2 LIG 1 112 -3.073 59.794 0.252
> ATOM 113 H58 LIG 1 113 -0.231 64.850 -1.169
> ATOM 114 C47 LIG 1 114 -2.514 57.757 -0.088
> ATOM 115 C48 LIG 1 115 -1.767 56.542 -0.565
> ATOM 116 H59 LIG 1 116 -2.179 55.599 -0.149
> ATOM 117 H60 LIG 1 117 -0.694 56.574 -0.275
> ATOM 118 H61 LIG 1 118 -1.833 56.471 -1.674
> ATOM 119 N3 LIG 1 119 -1.264 61.754 -0.663
> ATOM 120 H62 LIG 1 120 -0.462 58.600 -1.308
> ATOM 121 C49 LIG 1 121 -3.647 57.765 0.619
> ATOM 122 C50 LIG 1 122 -4.352 56.527 1.098
> ATOM 123 C51 LIG 1 123 -5.305 60.741 1.789
> ATOM 124 C52 LIG 1 124 -5.019 59.470 1.505
> ATOM 125 C53 LIG 1 125 -4.792 64.094 1.769
> ATOM 126 C54 LIG 1 126 -5.857 64.772 2.619
> ATOM 127 C55 LIG 1 127 -6.747 63.602 3.094
> ATOM 128 C56 LIG 1 128 -6.152 62.522 2.555
> ATOM 129 C57 LIG 1 129 -5.082 62.807 1.838
> ATOM 130 C58 LIG 1 130 1.522 63.220 -2.495
> ATOM 131 C59 LIG 1 131 1.546 60.060 -2.212
> ATOM 132 C60 LIG 1 132 1.366 59.705 -3.683
> ATOM 133 O4 LIG 1 133 2.844 60.528 -1.995
> ATOM 134 C61 LIG 1 134 -2.101 65.973 0.214
> ATOM 135 C62 LIG 1 135 -0.900 66.601 0.929
> ATOM 136 H63 LIG 1 136 -3.111 66.291 2.139
> ATOM 137 H64 LIG 1 137 -4.664 55.910 0.226
> ATOM 138 H65 LIG 1 138 -5.250 56.713 1.719
> ATOM 139 H66 LIG 1 139 -5.702 58.716 1.913
> ATOM 140 H67 LIG 1 140 -6.511 65.451 2.039
> ATOM 141 H68 LIG 1 141 -5.404 65.280 3.497
> ATOM 142 H69 LIG 1 142 1.108 64.209 -2.779
> ATOM 143 H70 LIG 1 143 1.830 62.749 -3.453
> ATOM 144 H71 LIG 1 144 2.424 63.415 -1.885
> ATOM 145 H72 LIG 1 145 1.516 59.113 -1.634
> ATOM 146 H73 LIG 1 146 0.381 59.220 -3.865
> ATOM 147 H74 LIG 1 147 2.166 59.017 -4.038
> ATOM 148 H75 LIG 1 148 1.411 60.626 -4.301
> ATOM 149 H76 LIG 1 149 -2.274 66.485 -0.763
> ATOM 150 H77 LIG 1 150 -0.001 66.613 0.278
> ATOM 151 H78 LIG 1 151 -0.650 66.042 1.859
> ATOM 152 H79 LIG 1 152 -1.111 67.657 1.209
> ATOM 153 O5 LIG 1 153 -7.742 63.642 3.776
> ATOM 154 C63 LIG 1 154 -6.326 61.202 2.546
> ATOM 155 C64 LIG 1 155 -7.398 60.445 3.243
> ATOM 156 H80 LIG 1 156 -7.638 59.480 2.751
> ATOM 157 H81 LIG 1 157 -8.327 61.050 3.277
> ATOM 158 H82 LIG 1 158 -7.051 60.249 4.279
> ATOM 159 H83 LIG 1 159 2.932 61.392 -2.346
> ATOM 160 H84 LIG 1 160 -3.662 55.928 1.731
> ATOM 161 C65 LIG 1 161 6.899 60.995 -1.795
> ATOM 162 C66 LIG 1 162 6.668 59.669 -1.904
> ATOM 163 C67 LIG 1 163 5.532 59.375 -1.252
> ATOM 164 C68 LIG 1 164 5.836 61.514 -1.156
> ATOM 165 C69 LIG 1 165 4.959 58.181 -1.051
> ATOM 166 C70 LIG 1 166 3.860 57.888 -0.337
> ATOM 167 C71 LIG 1 167 2.400 56.580 0.954
> ATOM 168 C72 LIG 1 168 2.173 58.068 0.939
> ATOM 169 N4 LIG 1 169 1.665 60.970 1.319
> ATOM 170 C73 LIG 1 170 2.716 63.531 0.824
> ATOM 171 C74 LIG 1 171 4.488 63.312 -0.245
> ATOM 172 C75 LIG 1 172 5.534 62.792 -0.901
> ATOM 173 N5 LIG 1 173 3.061 58.673 0.256
> ATOM 174 N6 LIG 1 174 3.505 62.705 0.268
> ATOM 175 H85 LIG 1 175 5.471 57.311 -1.485
> ATOM 176 C76 LIG 1 176 4.338 64.633 -0.044
> ATOM 177 C77 LIG 1 177 5.238 65.739 -0.514
> ATOM 178 H86 LIG 1 178 5.017 66.713 -0.026
> ATOM 179 H87 LIG 1 179 5.116 65.877 -1.612
> ATOM 180 H88 LIG 1 180 6.304 65.513 -0.305
> ATOM 181 N7 LIG 1 181 5.035 60.514 -0.748
> ATOM 182 H89 LIG 1 182 6.237 63.534 -1.272
> ATOM 183 C78 LIG 1 183 3.216 64.772 0.668
> ATOM 184 C79 LIG 1 184 2.698 66.087 1.177
> ATOM 185 C80 LIG 1 185 1.093 62.035 1.712
> ATOM 186 C81 LIG 1 186 1.578 63.259 1.480
> ATOM 187 C82 LIG 1 187 1.175 58.644 1.621
> ATOM 188 C83 LIG 1 188 0.034 58.079 2.454
> ATOM 189 C84 LIG 1 189 -0.727 59.344 2.911
> ATOM 190 C85 LIG 1 190 0.002 60.357 2.409
> ATOM 191 C86 LIG 1 191 1.045 59.955 1.709
> ATOM 192 C87 LIG 1 192 7.543 58.707 -2.661
> ATOM 193 C88 LIG 1 193 8.148 61.656 -2.342
> ATOM 194 C89 LIG 1 194 8.391 63.155 -2.161
> ATOM 195 O6 LIG 1 195 9.300 60.981 -1.900
> ATOM 196 C90 LIG 1 196 3.409 56.454 -0.186
> ATOM 197 C91 LIG 1 197 2.756 55.958 -1.484
> ATOM 198 H90 LIG 1 198 1.455 56.023 0.746
> ATOM 199 H91 LIG 1 199 2.373 66.720 0.323
> ATOM 200 H92 LIG 1 200 3.504 66.620 1.730
> ATOM 201 H93 LIG 1 201 0.998 64.093 1.892
> ATOM 202 H94 LIG 1 202 0.385 57.541 3.360
> ATOM 203 H95 LIG 1 203 -0.658 57.445 1.863
> ATOM 204 H96 LIG 1 204 7.675 59.064 -3.704
> ATOM 205 H97 LIG 1 205 7.131 57.680 -2.730
> ATOM 206 H98 LIG 1 206 8.544 58.616 -2.193
> ATOM 207 H99 LIG 1 207 8.121 61.470 -3.441
> ATOM 208 H100 LIG 1 208 7.701 63.762 -2.783
> ATOM 209 H101 LIG 1 209 9.409 63.462 -2.482
> ATOM 210 H102 LIG 1 210 8.314 63.466 -1.100
> ATOM 211 H103 LIG 1 211 4.262 55.788 0.094
> ATOM 212 H104 LIG 1 212 3.481 55.957 -2.329
> ATOM 213 H105 LIG 1 213 1.899 56.602 -1.779
> ATOM 214 H106 LIG 1 214 2.379 54.917 -1.365
> ATOM 215 O7 LIG 1 215 -1.734 59.396 3.573
> ATOM 216 C92 LIG 1 216 -0.017 61.692 2.412
> ATOM 217 C93 LIG 1 217 -1.042 62.545 3.084
> ATOM 218 H107 LIG 1 218 -0.983 62.392 4.182
> ATOM 219 H108 LIG 1 219 -2.054 62.234 2.747
> ATOM 220 H109 LIG 1 220 -0.936 63.628 2.866
> ATOM 221 H110 LIG 1 221 10.049 61.415 -2.275
> ATOM 222 H111 LIG 1 222 1.861 66.002 1.898
> ATOM 223 MG1 LIG 1 223 -3.169 61.830 0.000
> ATOM 224 MG2 LIG 1 224 3.169 60.710 0.000
> TER
> ATOM 225 C LIG 1 225 10.201 66.243 -0.109
> ATOM 226 C1 LIG 1 226 10.558 67.647 0.379
> ATOM 227 H LIG 1 227 10.810 65.994 -0.986
> ATOM 228 H1 LIG 1 228 9.141 66.207 -0.381
> ATOM 229 H2 LIG 1 229 11.618 67.683 0.652
> ATOM 230 H3 LIG 1 230 9.949 67.894 1.257
> ATOM 231 C2 LIG 1 231 10.284 68.660 -0.733
> ATOM 232 O LIG 1 232 9.689 68.309 -1.747
> ATOM 233 O1 LIG 1 233 10.716 69.995 -0.594
> ATOM 234 C3 LIG 1 234 11.249 70.337 -1.854
> ATOM 235 H4 LIG 1 235 12.079 69.665 -2.093
> ATOM 236 H5 LIG 1 236 10.470 70.241 -2.617
> ATOM 237 C4 LIG 1 237 11.753 71.782 -1.816
> ATOM 238 C5 LIG 1 238 12.345 72.417 -3.075
> ATOM 239 C6 LIG 1 239 12.432 71.608 -4.371
> ATOM 240 C7 LIG 1 240 12.851 73.861 -3.037
> ATOM 241 C8 LIG 1 241 12.683 74.494 -4.420
> ATOM 242 H6 LIG 1 242 11.692 72.360 -0.888
> ATOM 243 H7 LIG 1 243 13.204 70.839 -4.270
> ATOM 244 H8 LIG 1 244 11.465 71.132 -4.571
> ATOM 245 H9 LIG 1 245 12.688 72.275 -5.200
> ATOM 246 H10 LIG 1 246 13.909 73.871 -2.757
> ATOM 247 H11 LIG 1 247 12.273 74.431 -2.303
> ATOM 248 H12 LIG 1 248 11.625 74.484 -4.702
> ATOM 249 H13 LIG 1 249 13.261 73.924 -5.155
> ATOM 250 C9 LIG 1 250 13.188 75.939 -4.383
> ATOM 251 C10 LIG 1 251 13.780 76.574 -5.642
> ATOM 252 H14 LIG 1 252 13.126 76.518 -3.455
> ATOM 253 C11 LIG 1 253 13.868 75.765 -6.937
> ATOM 254 H15 LIG 1 254 14.639 74.996 -6.837
> ATOM 255 H16 LIG 1 255 12.902 75.289 -7.137
> ATOM 256 H17 LIG 1 256 14.123 76.431 -7.768
> ATOM 257 C12 LIG 1 257 14.284 78.017 -5.606
> ATOM 258 C13 LIG 1 258 14.119 78.651 -6.987
> ATOM 259 H18 LIG 1 259 13.709 78.587 -4.870
> ATOM 260 H19 LIG 1 260 15.345 78.029 -5.324
> ATOM 261 H20 LIG 1 261 13.061 78.640 -7.269
> ATOM 262 H21 LIG 1 262 14.695 78.080 -7.723
> ATOM 263 C14 LIG 1 263 14.623 80.094 -6.949
> ATOM 264 C15 LIG 1 264 15.137 80.648 -8.046
> ATOM 265 C16 LIG 1 265 15.644 82.092 -8.009
> ATOM 266 C17 LIG 1 266 15.227 79.839 -9.342
> ATOM 267 H22 LIG 1 267 14.562 80.673 -6.023
> ATOM 268 H23 LIG 1 268 15.067 82.662 -7.273
> ATOM 269 H24 LIG 1 269 16.702 82.102 -7.727
> ATOM 270 H25 LIG 1 270 15.525 82.546 -8.998
> ATOM 271 H26 LIG 1 271 15.997 79.071 -9.240
> ATOM 272 H27 LIG 1 272 14.259 79.361 -9.540
> ATOM 273 H28 LIG 1 273 15.481 80.505 -10.172
> ATOM 274 C18 LIG 1 274 13.508 54.073 2.226
> ATOM 275 C19 LIG 1 275 12.756 52.792 1.855
> ATOM 276 H29 LIG 1 276 14.296 53.839 2.949
> ATOM 277 H30 LIG 1 277 12.809 54.792 2.667
> ATOM 278 H31 LIG 1 278 13.455 52.074 1.414
> ATOM 279 H32 LIG 1 279 11.969 53.026 1.131
> ATOM 280 C20 LIG 1 280 12.132 52.187 3.112
> ATOM 281 O2 LIG 1 281 12.131 52.820 4.163
> ATOM 282 O3 LIG 1 282 11.554 50.901 3.065
> ATOM 283 C21 LIG 1 283 11.984 50.266 4.246
> ATOM 284 H33 LIG 1 284 13.078 50.219 4.259
> ATOM 285 H34 LIG 1 285 11.633 50.836 5.115
> ATOM 286 C22 LIG 1 286 11.411 48.848 4.299
> ATOM 287 C23 LIG 1 287 11.695 47.954 5.507
> ATOM 288 C24 LIG 1 288 12.550 48.478 6.662
> ATOM 289 C25 LIG 1 289 11.121 46.536 5.558
> ATOM 290 C26 LIG 1 290 10.876 46.139 7.016
> ATOM 291 H35 LIG 1 291 10.798 48.473 3.471
> ATOM 292 H36 LIG 1 292 13.596 48.550 6.339
> ATOM 293 H37 LIG 1 293 12.193 49.466 6.963
> ATOM 294 H38 LIG 1 294 12.477 47.790 7.511
> ATOM 295 H39 LIG 1 295 11.833 45.837 5.106
> ATOM 296 H40 LIG 1 296 10.175 46.503 5.005
> ATOM 297 H41 LIG 1 297 10.165 46.837 7.469
> ATOM 298 H42 LIG 1 298 11.820 46.172 7.567
> ATOM 299 C27 LIG 1 299 10.301 44.721 7.068
> ATOM 300 C28 LIG 1 300 10.587 43.827 8.276
> ATOM 301 H43 LIG 1 301 9.688 44.346 6.241
> ATOM 302 C29 LIG 1 302 11.442 44.350 9.431
> ATOM 303 H44 LIG 1 303 12.485 44.424 9.108
> ATOM 304 H45 LIG 1 304 11.084 45.339 9.731
> ATOM 305 H46 LIG 1 305 11.370 43.662 10.279
> ATOM 306 C30 LIG 1 306 10.013 42.408 8.328
> ATOM 307 C31 LIG 1 307 9.768 42.012 9.785
> ATOM 308 H47 LIG 1 308 9.068 42.376 7.776
> ATOM 309 H48 LIG 1 309 10.723 41.709 7.875
> ATOM 310 H49 LIG 1 310 9.056 42.711 10.238
> ATOM 311 H50 LIG 1 311 10.712 42.046 10.338
> ATOM 312 C32 LIG 1 312 9.195 40.594 9.836
> ATOM 313 C33 LIG 1 313 9.440 39.816 10.887
> ATOM 314 C34 LIG 1 314 8.869 38.398 10.940
> ATOM 315 C35 LIG 1 315 10.297 40.339 12.043
> ATOM 316 H51 LIG 1 316 8.581 40.220 9.010
> ATOM 317 H52 LIG 1 317 7.923 38.366 10.389
> ATOM 318 H53 LIG 1 318 9.578 37.700 10.486
> ATOM 319 H54 LIG 1 319 8.691 38.114 11.983
> ATOM 320 H55 LIG 1 320 11.342 40.412 11.720
> ATOM 321 H56 LIG 1 321 9.940 41.330 12.344
> ATOM 322 H57 LIG 1 322 10.224 39.652 12.892
> ATOM 323 C36 LIG 1 323 13.186 59.578 -1.719
> ATOM 324 C37 LIG 1 324 13.476 60.891 -1.773
> ATOM 325 C38 LIG 1 325 12.517 61.545 -1.096
> ATOM 326 C39 LIG 1 326 12.001 59.457 -1.104
> ATOM 327 C40 LIG 1 327 12.436 62.849 -0.804
> ATOM 328 C41 LIG 1 328 11.503 63.487 -0.078
> ATOM 329 C42 LIG 1 329 10.448 65.254 1.086
> ATOM 330 C43 LIG 1 330 9.779 63.905 1.092
> ATOM 331 N LIG 1 331 8.335 61.332 1.407
> ATOM 332 C44 LIG 1 332 8.419 58.585 0.805
> ATOM 333 C45 LIG 1 333 10.141 58.205 -0.266
> ATOM 334 C46 LIG 1 334 11.305 58.332 -0.911
> ATOM 335 N1 LIG 1 335 10.432 63.034 0.427
> ATOM 336 N2 LIG 1 336 9.432 59.118 0.252
> ATOM 337 H58 LIG 1 337 13.263 63.471 -1.169
> ATOM 338 C47 LIG 1 338 9.555 57.009 -0.088
> ATOM 339 C48 LIG 1 339 10.033 55.666 -0.565
> ATOM 340 H59 LIG 1 340 9.434 54.829 -0.149
> ATOM 341 H60 LIG 1 341 11.089 55.474 -0.275
> ATOM 342 H61 LIG 1 342 9.953 55.610 -1.674
> ATOM 343 N3 LIG 1 343 11.609 60.658 -0.663
> ATOM 344 H62 LIG 1 344 11.737 57.407 -1.308
> ATOM 345 C49 LIG 1 345 8.448 57.253 0.619
> ATOM 346 C50 LIG 1 346 7.501 56.189 1.098
> ATOM 347 C51 LIG 1 347 7.446 60.508 1.789
> ATOM 348 C52 LIG 1 348 7.461 59.206 1.505
> ATOM 349 C53 LIG 1 349 8.645 63.681 1.769
> ATOM 350 C54 LIG 1 350 7.744 64.565 2.619
> ATOM 351 C55 LIG 1 351 6.631 63.606 3.094
> ATOM 352 C56 LIG 1 352 6.988 62.426 2.555
> ATOM 353 C57 LIG 1 353 8.094 62.482 1.838
> ATOM 354 C58 LIG 1 354 14.638 61.513 -2.495
> ATOM 355 C59 LIG 1 355 14.004 58.417 -2.212
> ATOM 356 C60 LIG 1 356 13.755 58.107 -3.683
> ATOM 357 O4 LIG 1 357 15.371 58.605 -1.995
> ATOM 358 C61 LIG 1 358 11.668 64.959 0.214
> ATOM 359 C62 LIG 1 359 12.973 65.323 0.929
> ATOM 360 H63 LIG 1 360 10.746 65.480 2.139
> ATOM 361 H64 LIG 1 361 7.068 55.650 0.226
> ATOM 362 H65 LIG 1 362 6.662 56.557 1.719
> ATOM 363 H66 LIG 1 363 6.636 58.610 1.913
> ATOM 364 H67 LIG 1 364 7.246 65.365 2.039
> ATOM 365 H68 LIG 1 365 8.293 64.968 3.497
> ATOM 366 H69 LIG 1 366 14.439 62.566 -2.779
> ATOM 367 H70 LIG 1 367 14.842 60.988 -3.453
> ATOM 368 H71 LIG 1 368 15.561 61.516 -1.885
> ATOM 369 H72 LIG 1 369 13.778 57.497 -1.634
> ATOM 370 H73 LIG 1 370 12.690 57.838 -3.865
> ATOM 371 H74 LIG 1 371 14.394 57.268 -4.038
> ATOM 372 H75 LIG 1 372 13.990 58.999 -4.301
> ATOM 373 H76 LIG 1 373 11.605 65.495 -0.763
> ATOM 374 H77 LIG 1 374 13.855 65.148 0.278
> ATOM 375 H78 LIG 1 375 13.101 64.724 1.859
> ATOM 376 H79 LIG 1 376 12.986 66.400 1.209
> ATOM 377 O5 LIG 1 377 5.666 63.852 3.776
> ATOM 378 C63 LIG 1 378 6.543 61.171 2.546
> ATOM 379 C64 LIG 1 379 5.337 60.654 3.243
> ATOM 380 H80 LIG 1 380 4.902 59.760 2.751
> ATOM 381 H81 LIG 1 381 4.555 61.439 3.277
> ATOM 382 H82 LIG 1 382 5.636 60.390 4.279
> ATOM 383 H83 LIG 1 383 15.637 59.432 -2.346
> ATOM 384 H84 LIG 1 384 8.052 55.459 1.731
> ATOM 385 C65 LIG 1 385 19.434 58.218 -1.795
> ATOM 386 C66 LIG 1 386 18.932 56.969 -1.904
> ATOM 387 C67 LIG 1 387 17.760 56.918 -1.252
> ATOM 388 C68 LIG 1 388 18.503 58.947 -1.156
> ATOM 389 C69 LIG 1 389 16.952 55.870 -1.051
> ATOM 390 C70 LIG 1 390 15.816 55.812 -0.337
> ATOM 391 C71 LIG 1 391 14.116 54.836 0.954
> ATOM 392 C72 LIG 1 392 14.203 56.339 0.939
> ATOM 393 N4 LIG 1 393 14.310 59.282 1.319
> ATOM 394 C73 LIG 1 394 15.871 61.568 0.824
> ATOM 395 C74 LIG 1 395 17.558 60.986 -0.245
> ATOM 396 C75 LIG 1 396 18.473 60.260 -0.901
> ATOM 397 N5 LIG 1 397 15.198 56.746 0.256
> ATOM 398 N6 LIG 1 398 16.471 60.596 0.268
> ATOM 399 H85 LIG 1 399 17.271 54.912 -1.485
> ATOM 400 C76 LIG 1 400 17.686 62.309 -0.044
> ATOM 401 C77 LIG 1 401 18.796 63.203 -0.514
> ATOM 402 H86 LIG 1 402 18.783 64.202 -0.026
> ATOM 403 H87 LIG 1 403 18.706 63.364 -1.612
> ATOM 404 H88 LIG 1 404 19.792 62.760 -0.305
> ATOM 405 N7 LIG 1 405 17.511 58.135 -0.748
> ATOM 406 H89 LIG 1 406 19.315 60.839 -1.272
> ATOM 407 C78 LIG 1 407 16.618 62.678 0.668
> ATOM 408 C79 LIG 1 408 16.385 64.072 1.177
> ATOM 409 C80 LIG 1 409 13.972 60.443 1.712
> ATOM 410 C81 LIG 1 410 14.701 61.539 1.480
> ATOM 411 C82 LIG 1 411 13.347 57.109 1.621
> ATOM 412 C83 LIG 1 412 12.114 56.794 2.454
> ATOM 413 C84 LIG 1 413 11.633 58.190 2.911
> ATOM 414 C85 LIG 1 414 12.556 59.029 2.409
> ATOM 415 C86 LIG 1 415 13.493 58.419 1.709
> ATOM 416 C87 LIG 1 416 19.588 55.847 -2.661
> ATOM 417 C88 LIG 1 417 20.793 58.605 -2.342
> ATOM 418 C89 LIG 1 418 21.343 60.020 -2.161
> ATOM 419 O6 LIG 1 419 21.779 57.705 -1.900
> ATOM 420 C90 LIG 1 420 15.076 54.503 -0.186
> ATOM 421 C91 LIG 1 421 14.335 54.154 -1.484
> ATOM 422 H90 LIG 1 422 13.076 54.488 0.746
> ATOM 423 H91 LIG 1 423 16.199 64.759 0.323
> ATOM 424 H92 LIG 1 424 17.284 64.426 1.730
> ATOM 425 H93 LIG 1 425 14.307 62.475 1.892
> ATOM 426 H94 LIG 1 426 12.345 56.195 3.360
> ATOM 427 H95 LIG 1 427 11.305 56.318 1.863
> ATOM 428 H96 LIG 1 428 19.791 56.168 -3.704
> ATOM 429 H97 LIG 1 429 18.972 54.928 -2.730
> ATOM 430 H98 LIG 1 430 20.548 55.549 -2.193
> ATOM 431 H99 LIG 1 431 20.728 58.428 -3.441
> ATOM 432 H100 LIG 1 432 20.794 60.757 -2.783
> ATOM 433 H101 LIG 1 433 22.402 60.109 -2.482
> ATOM 434 H102 LIG 1 434 21.332 60.340 -1.100
> ATOM 435 H103 LIG 1 435 15.772 53.674 0.094
> ATOM 436 H104 LIG 1 436 15.043 54.002 -2.329
> ATOM 437 H105 LIG 1 437 13.630 54.962 -1.779
> ATOM 438 H106 LIG 1 438 13.749 53.214 -1.365
> ATOM 439 O7 LIG 1 439 10.659 58.450 3.573
> ATOM 440 C92 LIG 1 440 12.815 60.338 2.412
> ATOM 441 C93 LIG 1 441 11.990 61.386 3.084
> ATOM 442 H107 LIG 1 442 12.016 61.224 4.182
> ATOM 443 H108 LIG 1 443 10.936 61.292 2.747
> ATOM 444 H109 LIG 1 444 12.319 62.423 2.866
> ATOM 445 H110 LIG 1 445 22.602 57.974 -2.275
> ATOM 446 H111 LIG 1 446 15.548 64.163 1.898
> ATOM 447 MG1 LIG 1 447 9.761 61.129 0.000
> ATOM 448 MG2 LIG 1 448 15.727 58.715 0.000
> END
>
> Any help much appreciated.
>
> With thanks,
> Jenny
>
>
>> On Tue, Nov 08, 2011, Jennifer Brookes wrote:
>>>
>>> I guess I do not understand the problem of duplicates in leap. From
>>> your email it seems that the residue number, res name and atom name
>>> (combination)
>>> must be unique.
>>>
>>> At the moment in my .pdb I have the atom numbers 1- 13440 (60x224),
>>> though each dimer of 224 atoms is separated by TER, resname LIG (for
>>> all
>>> dimers)
>>> and residue number 1 (again for all dimers). So for the combination
>>> of these three fields there should be no duplicates.
>>>
>>> I actually have never been able to load a .pdb file
>>
>> What you have sounds fine. Can you either tell us what error
>> messages you are getting, or post the pdb file itself? As Carlos
>> said, it sounds like you have everything you need: in leap you would
>> load the library and frcmod files for the dimer, then use loadPdb to
>> load the 60-mer pdb file, then saveamberparm to save the prmtop file.
>> If one of these steps is failing (e.g. the loadPdb
>> step) is failing, we need to see the exact error messages.
>>
>> (Trying to use addles for this purpose is not going to work.)
>>
>> ....dac
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Wed Nov 09 2011 - 15:00:03 PST