AMBER Archive (2005)

Subject: Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production?

From: gtg549i_at_mail.gatech.edu
Date: Tue Nov 22 2005 - 15:28:36 CST

One more question, When i use the following script:

trajin cool_17500.crd.gz
trajout closest1.pdb pdb
center :1 mass origin
image origin center familiar
solvent byres :MAA
closest 2 :1 first noimage
solvent byres :DVB
closest 8 :1 first noimage
solvent byres :ACN
closest 11 :1 first noimage

I found there is sth wrong with the output pdb file. When i open the
closest1.pdb by VMD, some residues are separated or bonds are missing.

ATOM 1 C7 BE2 1 -0.783 0.404 -3.321 0.00 0.00
ATOM 2 C9 BE2 1 -2.215 0.750 -3.806 0.00 0.00
ATOM 3 C5 BE2 1 -3.114 0.777 -2.543 0.00 0.00
ATOM 4 O1 BE2 1 -4.091 1.816 -2.627 0.00 0.00
ATOM 5 H14 BE2 1 -4.741 1.551 -3.303 0.00 0.00
ATOM 6 H9 BE2 1 -3.618 -0.189 -2.450 0.00 0.00
ATOM 7 H15 BE2 1 -2.581 -0.007 -4.503 0.00 0.00
ATOM 8 H16 BE2 1 -2.218 1.716 -4.314 0.00 0.00
ATOM 9 H10 BE2 1 -0.129 1.274 -3.407 0.00 0.00
ATOM 10 H11 BE2 1 -0.353 -0.418 -3.897 0.00 0.00
ATOM 11 C3 BE2 1 -0.986 0.021 -1.845 0.00 0.00
ATOM 12 H3 BE2 1 -1.373 -1.000 -1.860 0.00 0.00
ATOM 13 C2 BE2 1 -2.122 0.949 -1.365 0.00 0.00
ATOM 14 C1 BE2 1 -1.698 2.448 -1.224 0.00 0.00
ATOM 15 H4 BE2 1 -1.392 2.876 -2.181 0.00 0.00
ATOM 16 H5 BE2 1 -0.874 2.593 -0.521 0.00 0.00
ATOM 17 H6 BE2 1 -2.535 3.043 -0.852 0.00 0.00
ATOM 18 C4 BE2 1 -2.623 0.413 -0.003 0.00 0.00
ATOM 19 H7 BE2 1 -3.413 1.059 0.387 0.00 0.00
ATOM 20 H8 BE2 1 -3.062 -0.577 -0.139 0.00 0.00
ATOM 21 C8 BE2 1 -1.465 0.310 1.030 0.00 0.00
ATOM 22 H12 BE2 1 -1.135 1.308 1.327 0.00 0.00
ATOM 23 H13 BE2 1 -1.878 -0.165 1.922 0.00 0.00
ATOM 24 C10 BE2 1 -0.234 -0.503 0.511 0.00 0.00
ATOM 25 H2 BE2 1 -0.612 -1.514 0.348 0.00 0.00
ATOM 26 C6 BE2 1 0.230 0.019 -0.885 0.00 0.00
ATOM 27 H1 BE2 1 0.621 1.033 -0.783 0.00 0.00
ATOM 28 C11 BE2 1 1.385 -0.871 -1.393 0.00 0.00
ATOM 29 H17 BE2 1 1.062 -1.913 -1.440 0.00 0.00
ATOM 30 H18 BE2 1 1.691 -0.572 -2.398 0.00 0.00
ATOM 31 C13 BE2 1 2.587 -0.738 -0.439 0.00 0.00
ATOM 32 H19 BE2 1 3.311 -1.519 -0.680 0.00 0.00
ATOM 33 H20 BE2 1 3.081 0.216 -0.636 0.00 0.00
ATOM 34 C14 BE2 1 2.251 -0.795 1.047 0.00 0.00
ATOM 35 C12 BE2 1 0.927 -0.669 1.505 0.00 0.00
ATOM 36 C15 BE2 1 0.682 -0.767 2.882 0.00 0.00
ATOM 37 H21 BE2 1 -0.330 -0.718 3.276 0.00 0.00
ATOM 38 C17 BE2 1 1.730 -0.944 3.782 0.00 0.00
ATOM 39 H23 BE2 1 1.526 -1.016 4.847 0.00 0.00
ATOM 40 C18 BE2 1 3.035 -1.039 3.323 0.00 0.00
ATOM 41 O2 BE2 1 4.042 -1.221 4.216 0.00 0.00
ATOM 42 H24 BE2 1 4.901 -1.170 3.760 0.00 0.00
ATOM 43 C16 BE2 1 3.296 -0.965 1.960 0.00 0.00
ATOM 44 H22 BE2 1 4.318 -1.050 1.598 0.00 0.00
ATOM 45 C3 MAA 2 4.904 -8.795 -1.876 0.00 0.00
ATOM 46 H1 MAA 2 4.051 -8.787 -2.557 0.00 0.00
ATOM 47 H2 MAA 2 4.547 -9.086 -0.886 0.00 0.00
ATOM 48 H3 MAA 2 5.588 -9.575 -2.215 0.00 0.00
ATOM 49 C1 MAA 2 5.576 -7.435 -1.850 0.00 0.00
ATOM 50 C4 MAA 2 6.750 -7.237 -2.478 0.00 0.00
ATOM 51 H4 MAA 2 7.253 -8.036 -3.017 0.00 0.00
ATOM 52 H5 MAA 2 7.227 -6.260 -2.490 0.00 0.00
ATOM 53 C2 MAA 2 4.908 -6.299 -1.150 0.00 0.00
ATOM 54 O2 MAA 2 3.780 -6.570 -0.581 0.00 0.00
ATOM 55 H6 MAA 2 3.507 -5.684 -0.284 0.00 0.00
ATOM 56 O1 MAA 2 5.356 -5.176 -1.079 0.00 0.00
ATOM 57 C3 MAA 3 -2.825 -4.880 -11.333 0.00 0.00
ATOM 58 H1 MAA 3 -3.325 -4.004 -10.914 0.00 0.00
ATOM 59 H2 MAA 3 -2.520 -4.629 -12.351 0.00 0.00
ATOM 60 H3 MAA 3 -1.918 -5.055 -10.751 0.00 0.00
ATOM 61 C1 MAA 3 -3.738 -6.089 -11.292 0.00 0.00
ATOM 62 C4 MAA 3 -4.155 -6.682 -12.430 0.00 0.00
ATOM 63 H4 MAA 3 -3.857 -6.310 -13.407 0.00 0.00
ATOM 64 H5 MAA 3 -4.807 -7.552 -12.425 0.00 0.00
ATOM 65 C2 MAA 3 -4.148 -6.578 -9.944 0.00 0.00
ATOM 66 O2 MAA 3 -4.970 -7.575 -9.925 0.00 0.00
ATOM 67 H6 MAA 3 -5.096 -7.697 -8.967 0.00 0.00
ATOM 68 O1 MAA 3 -3.756 -6.115 -8.897 0.00 0.00
ATOM 69 N1 ABN 4 -12.241 3.396 9.519 0.00 0.00
ATOM 70 C4 ABN 4 -13.298 3.487 9.778 0.00 0.00
ATOM 71 C1 ABN 4 -12.003 2.332 9.460 0.00 0.00
ATOM 72 C2 ABN 4 -12.111 3.821 8.522 0.00 0.00
ATOM 73 H1 ABN 4 -11.365 4.079 10.550 0.00 0.00
ATOM 74 H2 ABN 4 -10.415 4.960 10.176 0.00 0.00
ATOM 75 H3 ABN 4 -10.253 5.215 9.132 0.00 0.00
ATOM 76 C3 ABN 4 -9.777 5.460 10.901 0.00 0.00
ATOM 77 H4 ABN 4 -11.606 3.723 11.980 0.00 0.00
ATOM 78 H5 ABN 4 -10.810 4.263 12.845 0.00 0.00
ATOM 79 H6 ABN 4 -11.181 3.910 13.673 0.00 0.00
ATOM 80 N2 ABN 4 -12.477 2.977 12.363 0.00 0.00
ATOM 81 N3 ABN 4 6.790 12.190 10.476 0.00 0.00
ATOM 82 C5 ABN 4 6.074 12.766 9.886 0.00 0.00
ATOM 83 C7 ABN 4 7.710 12.775 10.535 0.00 0.00
ATOM 84 H7 ABN 4 6.390 12.089 11.488 0.00 0.00
ATOM 85 H8 ABN 4 7.050 10.826 9.868 0.00 0.00
ATOM 86 H9 ABN 4 6.262 10.348 8.885 0.00 0.00
ATOM 87 C8 ABN 4 5.420 10.917 8.502 0.00 0.00
ATOM 88 H10 ABN 4 6.425 9.370 8.439 0.00 0.00
ATOM 89 H11 ABN 4 8.199 10.048 10.414 0.00 0.00
ATOM 90 H12 ABN 4 8.406 8.891 9.879 0.00 0.00
ATOM 91 C6 ABN 4 9.183 8.579 10.376 0.00 0.00
ATOM 92 N4 ABN 4 8.929 10.435 11.296 0.00 0.00
ATOM 93 C1 DVB 5 4.904 -8.795 -1.876 0.00 0.00
ATOM 94 H1 DVB 5 4.051 -8.787 -2.557 0.00 0.00
ATOM 95 C2 DVB 5 4.547 -9.086 -0.886 0.00 0.00
ATOM 96 H2 DVB 5 5.588 -9.575 -2.215 0.00 0.00
ATOM 97 C3 DVB 5 5.576 -7.435 -1.850 0.00 0.00
ATOM 98 C9 DVB 5 6.750 -7.237 -2.478 0.00 0.00
ATOM 99 C10 DVB 5 7.253 -8.036 -3.017 0.00 0.00
ATOM 100 H9 DVB 5 7.227 -6.260 -2.490 0.00 0.00
ATOM 101 H10 DVB 5 4.908 -6.299 -1.150 0.00 0.00
ATOM 102 H8 DVB 5 3.780 -6.570 -0.581 0.00 0.00
ATOM 103 C4 DVB 5 3.507 -5.684 -0.284 0.00 0.00
ATOM 104 H3 DVB 5 5.356 -5.176 -1.079 0.00 0.00
ATOM 105 C5 DVB 5 -2.825 -4.880 -11.333 0.00 0.00
ATOM 106 H4 DVB 5 -3.325 -4.004 -10.914 0.00 0.00
ATOM 107 C6 DVB 5 -2.520 -4.629 -12.351 0.00 0.00
ATOM 108 C7 DVB 5 -1.918 -5.055 -10.751 0.00 0.00
ATOM 109 H5 DVB 5 -3.738 -6.089 -11.292 0.00 0.00
ATOM 110 C8 DVB 5 -4.155 -6.682 -12.430 0.00 0.00
ATOM 111 H6 DVB 5 -3.857 -6.310 -13.407 0.00 0.00
ATOM 112 H7 DVB 5 -4.807 -7.552 -12.425 0.00 0.00
ATOM 113 C1 DVB 6 10.581 1.725 -2.322 0.00 0.00
ATOM 114 H1 DVB 6 10.570 1.058 -3.187 0.00 0.00
ATOM 115 C2 DVB 6 11.511 1.541 -1.781 0.00 0.00
ATOM 116 H2 DVB 6 10.607 2.754 -2.686 0.00 0.00
ATOM 117 C3 DVB 6 9.371 1.501 -1.437 0.00 0.00
ATOM 118 C9 DVB 6 9.495 1.515 -0.096 0.00 0.00
ATOM 119 C10 DVB 6 10.458 1.682 0.381 0.00 0.00
ATOM 120 H9 DVB 6 8.646 1.361 0.565 0.00 0.00
ATOM 121 H10 DVB 6 8.061 1.270 -2.113 0.00 0.00
ATOM 122 H8 DVB 6 7.057 1.048 -1.329 0.00 0.00
ATOM 123 C4 DVB 6 6.347 0.855 -1.968 0.00 0.00
ATOM 124 H3 DVB 6 7.898 1.275 -3.312 0.00 0.00
ATOM 125 C5 DVB 6 -11.294 8.026 -1.362 0.00 0.00
ATOM 126 H4 DVB 6 -12.291 7.786 -1.738 0.00 0.00
ATOM 127 C6 DVB 6 -10.569 7.609 -2.064 0.00 0.00
ATOM 128 C7 DVB 6 -11.182 9.112 -1.381 0.00 0.00
ATOM 129 H5 DVB 6 -11.100 7.483 0.042 0.00 0.00
ATOM 130 C8 DVB 6 -10.188 6.526 0.293 0.00 0.00
ATOM 131 H6 DVB 6 -9.560 6.115 -0.493 0.00 0.00
ATOM 132 H7 DVB 6 -10.055 6.110 1.289 0.00 0.00
ATOM 133 C1 DVB 7 -13.503 -3.200 -9.642 0.00 0.00
ATOM 134 H1 DVB 7 -12.316 -3.760 -9.947 0.00 0.00
ATOM 135 C2 DVB 7 -12.024 -3.936 -10.979 0.00 0.00
ATOM 136 H2 DVB 7 -11.605 -4.063 -9.184 0.00 0.00
ATOM 137 C3 DVB 7 -13.919 -2.932 -8.234 0.00 0.00
ATOM 138 C9 DVB 7 -13.035 -3.187 -7.328 0.00 0.00
ATOM 139 C10 DVB 7 -13.514 -2.950 -6.514 0.00 0.00
ATOM 140 H9 DVB 7 -14.993 -2.481 -7.907 0.00 0.00
ATOM 141 H10 DVB 7 2.503 -10.312 -4.745 0.00 0.00
ATOM 142 H8 DVB 7 3.515 -10.786 -4.965 0.00 0.00
ATOM 143 C4 DVB 7 4.847 -11.338 -5.278 0.00 0.00
ATOM 144 H3 DVB 7 5.767 -10.196 -5.780 0.00 0.00
ATOM 145 C5 DVB 7 5.313 -9.693 -6.637 0.00 0.00
ATOM 146 H4 DVB 7 6.740 -10.576 -6.097 0.00 0.00
ATOM 147 C6 DVB 7 5.923 -9.455 -4.993 0.00 0.00
ATOM 148 C7 DVB 7 4.718 -12.441 -6.351 0.00 0.00
ATOM 149 H5 DVB 7 5.689 -12.900 -6.550 0.00 0.00
ATOM 150 C8 DVB 7 4.338 -12.028 -7.287 0.00 0.00
ATOM 151 H6 DVB 7 4.033 -13.224 -6.020 0.00 0.00
ATOM 152 H7 DVB 7 5.356 -11.963 -4.015 0.00 0.00
ATOM 153 C1 DVB 8 6.614 -12.190 -3.964 0.00 0.00
ATOM 154 H1 DVB 8 7.084 -12.990 -2.790 0.00 0.00
ATOM 155 C2 DVB 8 8.606 -12.760 -2.664 0.00 0.00
ATOM 156 H2 DVB 8 9.022 -13.339 -1.837 0.00 0.00
ATOM 157 C3 DVB 8 8.821 -11.705 -2.478 0.00 0.00
ATOM 158 C9 DVB 8 9.120 -13.054 -3.581 0.00 0.00
ATOM 159 C10 DVB 8 6.803 -14.484 -3.072 0.00 0.00
ATOM 160 H9 DVB 8 5.731 -14.664 -3.179 0.00 0.00
ATOM 161 H10 DVB 8 7.169 -15.110 -2.256 0.00 0.00
ATOM 162 H8 DVB 8 7.293 -14.804 -3.994 0.00 0.00
ATOM 163 C4 DVB 8 6.408 -12.558 -1.543 0.00 0.00
ATOM 164 H3 DVB 8 5.903 -12.281 -0.560 0.00 0.00
ATOM 165 C5 DVB 8 -5.998 -3.392 -9.271 0.00 0.00
ATOM 166 H4 DVB 8 -5.412 -4.079 -8.666 0.00 0.00
ATOM 167 C6 DVB 8 -5.492 -2.122 -9.540 0.00 0.00
ATOM 168 C7 DVB 8 -4.516 -1.856 -9.141 0.00 0.00
ATOM 169 H5 DVB 8 -6.221 -1.217 -10.318 0.00 0.00
ATOM 170 C8 DVB 8 -5.715 0.136 -10.653 0.00 0.00
ATOM 171 H6 DVB 8 -4.532 0.654 -10.279 0.00 0.00
ATOM 172 H7 DVB 8 -3.814 0.106 -9.675 0.00 0.00
ATOM 173 C1 DVB 9 -4.237 1.652 -10.594 0.00 0.00
ATOM 174 H1 DVB 9 -6.380 0.734 -11.275 0.00 0.00
ATOM 175 C2 DVB 9 -7.469 -1.609 -10.807 0.00 0.00
ATOM 176 H2 DVB 9 -8.055 -0.924 -11.414 0.00 0.00
ATOM 177 C3 DVB 9 -7.976 -2.879 -10.538 0.00 0.00
ATOM 178 C9 DVB 9 -8.947 -3.150 -10.943 0.00 0.00
ATOM 179 C10 DVB 9 -7.238 -3.788 -9.773 0.00 0.00
ATOM 180 H9 DVB 9 -7.720 -5.158 -9.477 0.00 0.00
ATOM 181 H10 DVB 9 -7.047 -5.768 -8.876 0.00 0.00
ATOM 182 H8 DVB 9 -8.886 -5.690 -9.877 0.00 0.00
ATOM 183 C4 DVB 9 -9.152 -6.708 -9.604 0.00 0.00
ATOM 184 H3 DVB 9 -9.616 -5.143 -10.468 0.00 0.00
ATOM 185 C5 DVB 9 -6.280 -1.807 2.591 0.00 0.00
ATOM 186 H4 DVB 9 -6.091 -1.228 1.691 0.00 0.00
ATOM 187 C6 DVB 9 -6.709 -3.130 2.476 0.00 0.00
ATOM 188 C7 DVB 9 -6.833 -3.557 1.483 0.00 0.00
ATOM 189 H5 DVB 9 -6.960 -3.895 3.619 0.00 0.00
ATOM 190 C8 DVB 9 -7.420 -5.305 3.553 0.00 0.00
ATOM 191 H6 DVB 9 -7.658 -6.009 2.434 0.00 0.00
ATOM 192 H7 DVB 9 -7.524 -5.595 1.438 0.00 0.00
ATOM 193 C1 DVB 10 -7.988 -7.043 2.490 0.00 0.00
ATOM 194 H1 DVB 10 -7.570 -5.786 4.518 0.00 0.00
ATOM 195 C2 DVB 10 -6.765 -3.313 4.871 0.00 0.00
ATOM 196 H2 DVB 10 -6.936 -3.895 5.773 0.00 0.00
ATOM 197 C3 DVB 10 -6.337 -1.991 4.985 0.00 0.00
ATOM 198 C9 DVB 10 -6.188 -1.577 5.979 0.00 0.00
ATOM 199 C10 DVB 10 -6.098 -1.221 3.844 0.00 0.00
ATOM 200 H9 DVB 10 -5.655 0.195 3.914 0.00 0.00
ATOM 201 H10 DVB 10 -5.501 0.678 2.950 0.00 0.00
ATOM 202 H8 DVB 10 -5.440 0.901 5.037 0.00 0.00
ATOM 203 C4 DVB 10 -5.118 1.938 4.988 0.00 0.00
ATOM 204 H3 DVB 10 -5.583 0.485 6.032 0.00 0.00
ATOM 205 C5 DVB 10 -12.001 -1.315 7.610 0.00 0.00
ATOM 206 H4 DVB 10 -11.836 -0.710 6.723 0.00 0.00
ATOM 207 C6 DVB 10 -12.720 -0.772 8.673 0.00 0.00
ATOM 208 C7 DVB 10 -13.092 0.245 8.583 0.00 0.00
ATOM 209 H5 DVB 10 -12.951 -1.519 9.830 0.00 0.00
ATOM 210 C8 DVB 10 -13.697 -0.978 10.994 0.00 0.00
ATOM 211 H6 DVB 10 -14.231 0.252 11.086 0.00 0.00
ATOM 212 H7 DVB 10 -14.160 0.988 10.289 0.00 0.00
ATOM 213 C1 DVB 11 -14.745 0.572 11.989 0.00 0.00
ATOM 214 H1 DVB 11 -13.796 -1.658 11.838 0.00 0.00
ATOM 215 C2 DVB 11 -12.447 -2.819 9.898 0.00 0.00
ATOM 216 H2 DVB 11 -12.603 -3.412 10.796 0.00 0.00
ATOM 217 C3 DVB 11 -11.722 -3.361 8.837 0.00 0.00
ATOM 218 C9 DVB 11 -11.334 -4.372 8.931 0.00 0.00
ATOM 219 C10 DVB 11 -11.490 -2.611 7.681 0.00 0.00
ATOM 220 H9 DVB 11 -10.717 -3.140 6.530 0.00 0.00
ATOM 221 H10 DVB 11 -10.611 -2.454 5.691 0.00 0.00
ATOM 222 H8 DVB 11 -10.153 -4.357 6.446 0.00 0.00
ATOM 223 C4 DVB 11 -9.601 -4.653 5.558 0.00 0.00
ATOM 224 H3 DVB 11 -10.214 -5.090 7.246 0.00 0.00
ATOM 225 C5 DVB 11 7.674 10.403 -3.585 0.00 0.00
ATOM 226 H4 DVB 11 7.062 10.447 -2.687 0.00 0.00
ATOM 227 C6 DVB 11 8.883 9.709 -3.555 0.00 0.00
ATOM 228 C7 DVB 11 9.185 9.225 -2.629 0.00 0.00
ATOM 229 H5 DVB 11 9.680 9.622 -4.700 0.00 0.00
ATOM 230 C8 DVB 11 10.963 8.874 -4.730 0.00 0.00
ATOM 231 H6 DVB 11 11.518 8.207 -3.703 0.00 0.00
ATOM 232 H7 DVB 11 11.063 8.154 -2.718 0.00 0.00
ATOM 233 C1 DVB 12 12.463 7.684 -3.830 0.00 0.00
ATOM 234 H1 DVB 12 11.477 8.878 -5.690 0.00 0.00
ATOM 235 C2 DVB 12 9.247 10.252 -5.867 0.00 0.00
ATOM 236 H2 DVB 12 9.844 10.183 -6.773 0.00 0.00
ATOM 237 C3 DVB 12 8.039 10.948 -5.897 0.00 0.00
ATOM 238 C9 DVB 12 7.727 11.407 -6.832 0.00 0.00
ATOM 239 C10 DVB 12 7.235 11.024 -4.755 0.00 0.00
ATOM 240 H9 DVB 12 5.929 11.730 -4.744 0.00 0.00
ATOM 241 H10 DVB 12 5.401 11.713 -3.792 0.00 0.00
ATOM 242 H8 DVB 12 5.364 12.365 -5.785 0.00 0.00
ATOM 243 C4 DVB 12 4.400 12.855 -5.681 0.00 0.00
ATOM 244 H3 DVB 12 5.825 12.414 -6.769 0.00 0.00
ATOM 245 C5 DVB 12 -12.227 2.822 -7.367 0.00 0.00
ATOM 246 H4 DVB 12 -11.678 3.730 -7.604 0.00 0.00
ATOM 247 C6 DVB 12 -13.506 2.926 -6.822 0.00 0.00
ATOM 248 C7 DVB 12 -13.915 3.916 -6.641 0.00 0.00
ATOM 249 H5 DVB 12 -14.240 1.776 -6.520 0.00 0.00
ATOM 250 C8 DVB 12 -15.606 1.826 -5.943 0.00 0.00
ATOM 251 H6 DVB 12 -16.298 2.937 -5.647 0.00 0.00
ATOM 252 H7 DVB 12 -15.904 3.938 -5.805 0.00 0.00
ATOM 253 C2 ACN 13 -2.369 -3.279 -1.096 0.00 0.00
ATOM 254 H1 ACN 13 -4.086 -3.925 -0.865 0.00 0.00
ATOM 255 H2 ACN 13 7.046 5.395 2.759 0.00 0.00
ATOM 256 H3 ACN 13 7.366 6.364 3.135 0.00 0.00
ATOM 257 C1 ACN 13 6.420 4.503 3.629 0.00 0.00
ATOM 258 O1 ACN 13 6.260 4.803 4.661 0.00 0.00
ATOM 259 C3 ACN 13 5.989 3.254 3.175 0.00 0.00
ATOM 260 H4 ACN 13 5.315 2.274 4.063 0.00 0.00
ATOM 261 H5 ACN 13 5.059 2.432 5.373 0.00 0.00
ATOM 262 H6 ACN 13 5.333 3.328 5.924 0.00 0.00
ATOM 263 C2 ACN 14 1.193 2.142 3.603 0.00 0.00
ATOM 264 H1 ACN 14 -0.388 2.153 4.557 0.00 0.00
ATOM 265 H2 ACN 14 -10.221 -7.760 9.935 0.00 0.00
ATOM 266 H3 ACN 14 -9.869 -8.507 9.228 0.00 0.00
ATOM 267 C1 ACN 14 -9.328 -7.233 10.867 0.00 0.00
ATOM 268 O1 ACN 14 -8.300 -7.587 10.868 0.00 0.00
ATOM 269 C3 ACN 14 -9.747 -6.261 11.778 0.00 0.00
ATOM 270 H4 ACN 14 -8.834 -5.650 12.773 0.00 0.00
ATOM 271 H5 ACN 14 -7.533 -5.936 12.940 0.00 0.00
ATOM 272 H6 ACN 14 -7.011 -6.675 12.337 0.00 0.00
ATOM 273 C2 ACN 15 -1.667 -0.232 6.219 0.00 0.00
ATOM 274 H1 ACN 15 -2.926 -0.827 4.999 0.00 0.00
ATOM 275 H2 ACN 15 3.287 7.950 -13.874 0.00 0.00
ATOM 276 H3 ACN 15 4.118 7.624 -14.495 0.00 0.00
ATOM 277 C1 ACN 15 2.733 7.061 -12.954 0.00 0.00
ATOM 278 O1 ACN 15 3.154 6.062 -12.876 0.00 0.00
ATOM 279 C3 ACN 15 1.663 7.455 -12.145 0.00 0.00
ATOM 280 H4 ACN 15 1.039 6.547 -11.150 0.00 0.00
ATOM 281 H5 ACN 15 1.392 5.273 -10.908 0.00 0.00
ATOM 282 H6 ACN 15 2.192 4.771 -11.446 0.00 0.00
ATOM 283 C2 ACN 16 4.558 1.649 5.937 0.00 0.00
ATOM 284 H1 ACN 16 5.010 1.347 3.579 0.00 0.00
ATOM 285 H2 ACN 16 6.198 2.919 1.836 0.00 0.00
ATOM 286 H3 ACN 16 5.872 1.953 1.460 0.00 0.00
ATOM 287 C1 ACN 16 6.826 3.811 0.967 0.00 0.00
ATOM 288 O1 ACN 16 6.965 3.515 -0.069 0.00 0.00
ATOM 289 C3 ACN 16 7.260 5.059 1.421 0.00 0.00
ATOM 290 H4 ACN 16 7.937 6.039 0.533 0.00 0.00
ATOM 291 H5 ACN 16 8.217 6.978 1.009 0.00 0.00
ATOM 292 H6 ACN 16 8.221 5.863 -0.768 0.00 0.00
ATOM 293 C2 ACN 17 4.558 1.649 5.937 0.00 0.00
ATOM 294 H1 ACN 17 5.010 1.347 3.579 0.00 0.00
ATOM 295 H2 ACN 17 6.198 2.919 1.836 0.00 0.00
ATOM 296 H3 ACN 17 5.872 1.953 1.460 0.00 0.00
ATOM 297 C1 ACN 17 6.826 3.811 0.967 0.00 0.00
ATOM 298 O1 ACN 17 6.965 3.515 -0.069 0.00 0.00
ATOM 299 C3 ACN 17 7.260 5.059 1.421 0.00 0.00
ATOM 300 H4 ACN 17 7.937 6.039 0.533 0.00 0.00
ATOM 301 H5 ACN 17 8.217 6.978 1.009 0.00 0.00
ATOM 302 H6 ACN 17 8.221 5.863 -0.768 0.00 0.00
ATOM 303 C2 ACN 18 -1.528 -5.890 -2.948 0.00 0.00
ATOM 304 H1 ACN 18 -0.602 -7.063 -4.037 0.00 0.00
ATOM 305 H2 ACN 18 10.446 13.293 -13.472 0.00 0.00
ATOM 306 H3 ACN 18 9.968 12.570 -14.128 0.00 0.00
ATOM 307 C1 ACN 18 10.517 13.023 -12.107 0.00 0.00
ATOM 308 O1 ACN 18 10.093 12.092 -11.739 0.00 0.00
ATOM 309 C3 ACN 18 11.126 13.930 -11.237 0.00 0.00
ATOM 310 H4 ACN 18 11.243 13.680 -9.778 0.00 0.00
ATOM 311 H5 ACN 18 10.799 12.595 -9.120 0.00 0.00
ATOM 312 H6 ACN 18 10.292 11.771 -9.616 0.00 0.00
ATOM 313 C2 ACN 19 7.506 -6.616 2.544 0.00 0.00
ATOM 314 H1 ACN 19 6.820 -8.443 3.983 0.00 0.00
ATOM 315 H2 ACN 19 7.738 -9.228 6.317 0.00 0.00
ATOM 316 H3 ACN 19 6.904 -9.800 5.916 0.00 0.00
ATOM 317 C1 ACN 19 8.270 -9.583 7.555 0.00 0.00
ATOM 318 O1 ACN 19 7.833 -10.425 8.086 0.00 0.00
ATOM 319 C3 ACN 19 9.339 -8.866 8.101 0.00 0.00
ATOM 320 H4 ACN 19 9.939 -9.204 9.416 0.00 0.00
ATOM 321 H5 ACN 19 10.767 -8.567 9.724 0.00 0.00
ATOM 322 H6 ACN 19 9.553 -10.201 10.232 0.00 0.00
ATOM 323 C2 ACN 20 7.506 -6.616 2.544 0.00 0.00
ATOM 324 H1 ACN 20 6.820 -8.443 3.983 0.00 0.00
ATOM 325 H2 ACN 20 7.738 -9.228 6.317 0.00 0.00
ATOM 326 H3 ACN 20 6.904 -9.800 5.916 0.00 0.00
ATOM 327 C1 ACN 20 8.270 -9.583 7.555 0.00 0.00
ATOM 328 O1 ACN 20 7.833 -10.425 8.086 0.00 0.00
ATOM 329 C3 ACN 20 9.339 -8.866 8.101 0.00 0.00
ATOM 330 H4 ACN 20 9.939 -9.204 9.416 0.00 0.00
ATOM 331 H5 ACN 20 10.767 -8.567 9.724 0.00 0.00
ATOM 332 H6 ACN 20 9.553 -10.201 10.232 0.00 0.00
ATOM 333 C2 ACN 21 -3.566 1.088 8.264 0.00 0.00
ATOM 334 H1 ACN 21 -2.643 -0.467 8.652 0.00 0.00
ATOM 335 H2 ACN 21 7.815 -12.673 -12.841 0.00 0.00
ATOM 336 H3 ACN 21 8.752 -13.214 -12.934 0.00 0.00
ATOM 337 C1 ACN 21 6.617 -13.331 -13.117 0.00 0.00
ATOM 338 O1 ACN 21 6.656 -14.373 -13.425 0.00 0.00
ATOM 339 C3 ACN 21 5.395 -12.666 -12.989 0.00 0.00
ATOM 340 H4 ACN 21 4.093 -13.328 -13.250 0.00 0.00
ATOM 341 H5 ACN 21 3.916 -14.607 -13.622 0.00 0.00
ATOM 342 H6 ACN 21 4.741 -15.299 -13.771 0.00 0.00
ATOM 343 C2 ACN 22 -8.931 3.722 1.872 0.00 0.00
ATOM 344 H1 ACN 22 -8.637 3.089 3.582 0.00 0.00
ATOM 345 H2 ACN 22 2.504 -4.163 -10.456 0.00 0.00
ATOM 346 H3 ACN 22 2.040 -4.187 -11.439 0.00 0.00
ATOM 347 C1 ACN 22 3.555 -3.279 -10.218 0.00 0.00
ATOM 348 O1 ACN 22 3.883 -2.631 -11.026 0.00 0.00
ATOM 349 C3 ACN 22 4.181 -3.240 -8.968 0.00 0.00
ATOM 350 H4 ACN 22 5.316 -2.330 -8.668 0.00 0.00
ATOM 351 H5 ACN 22 5.864 -1.444 -9.516 0.00 0.00
ATOM 352 H6 ACN 22 5.506 -1.305 -10.532 0.00 0.00
ATOM 353 C2 ACN 23 -4.237 1.652 -10.594 0.00 0.00
ATOM 354 H1 ACN 23 -6.380 0.734 -11.275 0.00 0.00
ATOM 355 H2 ACN 23 -7.469 -1.609 -10.807 0.00 0.00
ATOM 356 H3 ACN 23 -8.055 -0.924 -11.414 0.00 0.00
ATOM 357 C1 ACN 23 -7.976 -2.879 -10.538 0.00 0.00
ATOM 358 O1 ACN 23 -8.947 -3.150 -10.943 0.00 0.00
ATOM 359 C3 ACN 23 -7.238 -3.788 -9.773 0.00 0.00
ATOM 360 H4 ACN 23 -7.720 -5.158 -9.477 0.00 0.00
ATOM 361 H5 ACN 23 -7.047 -5.768 -8.876 0.00 0.00
ATOM 362 H6 ACN 23 -8.886 -5.690 -9.877 0.00 0.00

Is there anything wrong with my script?

If I output the file in trj format, how can i get the NEW prmtop file from the
trj file for the residues with selected solvent molecules?

Thanks a lot!

Shuting

Quoting Thomas Cheatham <cheatham_at_chpc.utah.edu>:

>
> > I wonder if anyone knows how to extract the residues of first solvation
> shell
> > from the simulated system after the production?
> >
> > My system contains a host, guests, solvent, I want to get the information
> > (prmtop or pdb) of the residue groups in the first solvation shell for the
> > mm_pbsa study. I wonder if there is a quite way to do that cause i have so
> > many snapshots. The only thing i can find in the manual is "watershell",
> but
> > it only give the number of residue included in the shell.
>
> The closest option will do this, saving the "n" number of solvent
> molecules closest to the solute of interest. If your solvent is residues
> named ETH and you want to save the closest 20 waters around residues 1-3,
>
> trajin mdcrd.1
> trajin mdcrd.2.gz
> trajout mdcrd_20closest.trj
> solvent byname ETH
> center :1-3 mass origin
> image origin center familiar
> closest 20 :1-3 first noimage
>
>
>
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