[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27
Justin A. Lemkul
jalemkul at vt.edu
Tue Jun 28 19:54:13 CEST 2011
Kalavera at gmx.net wrote:
> Dear gromacs users,
>
> I constructed a small *.pdb file comprised of only lipids (POPE bilayer). If I try to convert this pdb file with pdb2gmx (gromacs 4.5.4) and the included charmm27 forcefield, I get warnings for "missing hydrogen atoms" and "Long Bond" warnings.
>
pdb2gmx is ill-suited for dealing with multiple molecules. The better approach
is to work with a single POPE molecule with a suitably constructed .rtp entry
for it. pdb2gmx should then generate a topology for one lipid, which can then
be modified to be used in an #include statement or extended to accommodate an
entire bilayer simply by altering the [molecules] directive.
The errors you are seeing are likely due to naming mismatch or poor starting
geometry, but since you haven't quoted the errors, I don't dare guess beyond that.
> In other threads, the lipids.hdb is discussed in this context. In my case, all hydrogen atoms are available. Do I need to proceed the lipids.hdb (like described in the manual), or can I leave it empty ?
The .hdb file is only necessary to reconstruct missing H atoms. If your
structure has all of them and they are correctly named, then an .hdb is not
necessary.
-Justin
> The resnames are consistent with the lipids.rtp entries.
>
> Thanks for all your help,
>
> M.Kalavera
>
>
> --------------------Additional information--------------------------------
> Command used:
>
> pdb2gmx_mpi -f lipids.pdb -p lipids.top -o lipids.gro -water TIP3P -ff charmm27
>
> The first entries of my pdb file:
>
> REMARK
> ATOM 1 N POPE 1 -14.135 -21.952 22.035 1.00 0.00 LIPI
> ATOM 2 HN1 POPE 1 -14.125 -22.660 22.797 1.00 0.00 LIPI
> ATOM 3 HN2 POPE 1 -13.175 -21.821 21.659 1.00 0.00 LIPI
> ATOM 4 HN3 POPE 1 -14.339 -21.041 22.493 1.00 0.00 LIPI
> ATOM 5 C12 POPE 1 -15.154 -22.312 21.033 1.00 0.00 LIPI
> ATOM 6 H12A POPE 1 -16.107 -22.486 21.577 1.00 0.00 LIPI
> ATOM 7 H12B POPE 1 -14.920 -23.252 20.489 1.00 0.00 LIPI
> ATOM 8 C11 POPE 1 -15.234 -21.168 20.058 1.00 0.00 LIPI
> ATOM 9 H11A POPE 1 -14.276 -20.976 19.529 1.00 0.00 LIPI
> ATOM 10 H11B POPE 1 -15.909 -21.556 19.266 1.00 0.00 LIPI
> ATOM 11 P POPE 1 -15.310 -18.486 20.024 1.00 0.00 LIPI
> ATOM 12 O13 POPE 1 -16.549 -17.712 19.663 1.00 0.00 LIPI
> ATOM 13 O14 POPE 1 -14.314 -17.846 20.940 1.00 0.00 LIPI
> ATOM 14 O11 POPE 1 -14.637 -18.744 18.604 1.00 0.00 LIPI
> ATOM 15 O12 POPE 1 -15.752 -19.947 20.557 1.00 0.00 LIPI
> ATOM 16 C1 POPE 1 -14.267 -17.491 18.032 1.00 0.00 LIPI
> ATOM 17 HA POPE 1 -15.110 -16.900 17.614 1.00 0.00 LIPI
> ATOM 18 HB POPE 1 -13.690 -16.851 18.733 1.00 0.00 LIPI
> ATOM 19 C2 POPE 1 -13.395 -17.725 16.681 1.00 0.00 LIPI
> ATOM 20 HS POPE 1 -12.357 -17.976 16.987 1.00 0.00 LIPI
> ATOM 21 O21 POPE 1 -13.383 -16.549 15.849 1.00 0.00 LIPI
> ATOM 22 C21 POPE 1 -12.419 -16.414 14.956 1.00 0.00 LIPI
> ATOM 23 O22 POPE 1 -11.405 -17.098 14.835 1.00 0.00 LIPI
> ATOM 24 C22 POPE 1 -12.767 -15.262 13.918 1.00 0.00 LIPI
> ATOM 25 H2R POPE 1 -13.659 -15.556 13.324 1.00 0.00 LIPI
> ATOM 26 H2S POPE 1 -12.825 -14.275 14.427 1.00 0.00 LIPI
> ATOM 27 C3 POPE 1 -13.924 -18.925 15.834 1.00 0.00 LIPI
> ATOM 28 HX POPE 1 -13.196 -19.033 15.002 1.00 0.00 LIPI
> ATOM 29 HY POPE 1 -13.829 -19.915 16.331 1.00 0.00 LIPI
> ATOM 30 O31 POPE 1 -15.338 -18.716 15.377 1.00 0.00 LIPI
> ATOM 31 C31 POPE 1 -15.514 -19.308 14.227 1.00 0.00 LIPI
> ATOM 32 O32 POPE 1 -14.683 -19.825 13.544 1.00 0.00 LIPI
> ATOM 33 C32 POPE 1 -17.023 -19.166 13.689 1.00 0.00 LIPI
> ATOM 34 H2X POPE 1 -17.106 -20.050 13.022 1.00 0.00 LIPI
> ATOM 35 H2Y POPE 1 -17.627 -19.380 14.597 1.00 0.00 LIPI
> ATOM 36 C23 POPE 1 -11.614 -14.871 12.965 1.00 0.00 LIPI
> ATOM 37 H3R POPE 1 -11.533 -13.767 12.868 1.00 0.00 LIPI
> ATOM 38 H3S POPE 1 -10.669 -15.218 13.434 1.00 0.00 LIPI
> ATOM 39 C24 POPE 1 -11.678 -15.385 11.524 1.00 0.00 LIPI
> ATOM 40 H4R POPE 1 -12.586 -14.837 11.192 1.00 0.00 LIPI
> ATOM 41 H4S POPE 1 -10.819 -15.050 10.904 1.00 0.00 LIPI
> ATOM 42 C25 POPE 1 -12.001 -16.882 11.443 1.00 0.00 LIPI
> ATOM 43 H5R POPE 1 -11.079 -17.466 11.651 1.00 0.00 LIPI
> ATOM 44 H5S POPE 1 -12.770 -17.181 12.187 1.00 0.00 LIPI
> ATOM 45 C26 POPE 1 -12.435 -17.332 10.094 1.00 0.00 LIPI
> ATOM 46 H6R POPE 1 -12.808 -18.375 10.172 1.00 0.00 LIPI
> ATOM 47 H6S POPE 1 -13.247 -16.723 9.640 1.00 0.00 LIPI
> ATOM 48 C27 POPE 1 -11.179 -17.198 9.148 1.00 0.00 LIPI
> ATOM 49 H7R POPE 1 -10.668 -16.220 9.280 1.00 0.00 LIPI
> ATOM 50 H7S POPE 1 -10.407 -17.957 9.395 1.00 0.00 LIPI
> ATOM 51 C28 POPE 1 -11.573 -17.384 7.605 1.00 0.00 LIPI
> ATOM 52 H8R POPE 1 -12.256 -16.556 7.320 1.00 0.00 LIPI
> ATOM 53 H8S POPE 1 -10.612 -17.358 7.047 1.00 0.00 LIPI
> ATOM 54 C29 POPE 1 -12.262 -18.679 7.532 1.00 0.00 LIPI
> ATOM 55 H91 POPE 1 -11.685 -19.498 7.987 1.00 0.00 LIPI
> ATOM 56 C210 POPE 1 -13.523 -18.906 7.069 1.00 0.00 LIPI
> ATOM 57 H101 POPE 1 -14.026 -19.883 7.028 1.00 0.00 LIPI
> ATOM 58 C211 POPE 1 -14.472 -17.934 6.435 1.00 0.00 LIPI
> ATOM 59 H11R POPE 1 -15.424 -18.007 7.003 1.00 0.00 LIPI
> ATOM 60 H11S POPE 1 -14.170 -16.865 6.447 1.00 0.00 LIPI
> ATOM 61 C212 POPE 1 -14.750 -18.261 4.918 1.00 0.00 LIPI
> ATOM 62 H12R POPE 1 -13.797 -18.179 4.352 1.00 0.00 LIPI
> ATOM 63 H12S POPE 1 -15.149 -19.289 4.785 1.00 0.00 LIPI
> ATOM 64 C213 POPE 1 -15.756 -17.364 4.264 1.00 0.00 LIPI
> ATOM 65 H13R POPE 1 -16.769 -17.520 4.691 1.00 0.00 LIPI
> ATOM 66 H13S POPE 1 -15.470 -16.366 4.662 1.00 0.00 LIPI
> ATOM 67 C214 POPE 1 -15.787 -17.415 2.718 1.00 0.00 LIPI
> ATOM 68 H14R POPE 1 -14.803 -16.993 2.420 1.00 0.00 LIPI
> ATOM 69 H14S POPE 1 -15.977 -18.434 2.318 1.00 0.00 LIPI
> ATOM 70 C215 POPE 1 -16.823 -16.519 2.048 1.00 0.00 LIPI
> ATOM 71 H15R POPE 1 -17.829 -16.852 2.381 1.00 0.00 LIPI
> ATOM 72 H15S POPE 1 -16.676 -15.433 2.229 1.00 0.00 LIPI
> ATOM 73 C216 POPE 1 -16.797 -16.645 0.489 1.00 0.00 LIPI
> ATOM 74 H16R POPE 1 -15.771 -16.468 0.101 1.00 0.00 LIPI
> ATOM 75 H16S POPE 1 -17.118 -17.640 0.113 1.00 0.00 LIPI
> ATOM 76 C217 POPE 1 -17.792 -15.697 -0.156 1.00 0.00 LIPI
> ATOM 77 H17R POPE 1 -18.763 -16.230 -0.066 1.00 0.00 LIPI
> ATOM 78 H17S POPE 1 -17.746 -14.662 0.244 1.00 0.00 LIPI
> ATOM 79 C218 POPE 1 -17.473 -15.721 -1.669 1.00 0.00 LIPI
> ATOM 80 H18R POPE 1 -16.591 -15.052 -1.774 1.00 0.00 LIPI
> ATOM 81 H18S POPE 1 -17.038 -16.672 -2.044 1.00 0.00 LIPI
> ATOM 82 H18T POPE 1 -18.351 -15.355 -2.244 1.00 0.00 LIPI
> ATOM 83 C33 POPE 1 -17.263 -17.863 13.021 1.00 0.00 LIPI
> ATOM 84 H3X POPE 1 -18.337 -17.753 12.759 1.00 0.00 LIPI
> ATOM 85 H3Y POPE 1 -17.135 -16.996 13.704 1.00 0.00 LIPI
> ATOM 86 C34 POPE 1 -16.410 -17.562 11.765 1.00 0.00 LIPI
> ATOM 87 H4X POPE 1 -15.354 -17.327 12.018 1.00 0.00 LIPI
> ATOM 88 H4Y POPE 1 -16.387 -18.484 11.146 1.00 0.00 LIPI
> ATOM 89 C35 POPE 1 -16.833 -16.334 10.951 1.00 0.00 LIPI
> ATOM 90 H5X POPE 1 -17.925 -16.159 11.065 1.00 0.00 LIPI
> ATOM 91 H5Y POPE 1 -16.256 -15.483 11.371 1.00 0.00 LIPI
> ATOM 92 C36 POPE 1 -16.606 -16.326 9.426 1.00 0.00 LIPI
> ATOM 93 H6X POPE 1 -15.530 -16.353 9.151 1.00 0.00 LIPI
> ATOM 94 H6Y POPE 1 -17.037 -17.279 9.051 1.00 0.00 LIPI
> ATOM 95 C37 POPE 1 -17.335 -15.184 8.706 1.00 0.00 LIPI
> ATOM 96 H7X POPE 1 -18.428 -15.164 8.900 1.00 0.00 LIPI
> ATOM 97 H7Y POPE 1 -16.893 -14.303 9.217 1.00 0.00 LIPI
> ATOM 98 C38 POPE 1 -17.011 -15.122 7.240 1.00 0.00 LIPI
> ATOM 99 H8X POPE 1 -15.921 -14.914 7.192 1.00 0.00 LIPI
> ATOM 100 H8Y POPE 1 -17.159 -16.168 6.893 1.00 0.00 LIPI
> ATOM 101 C39 POPE 1 -17.912 -14.117 6.532 1.00 0.00 LIPI
> ATOM 102 H9X POPE 1 -18.916 -14.581 6.429 1.00 0.00 LIPI
> ATOM 103 H9Y POPE 1 -18.095 -13.292 7.254 1.00 0.00 LIPI
> ATOM 104 C310 POPE 1 -17.433 -13.541 5.200 1.00 0.00 LIPI
> ATOM 105 H10X POPE 1 -16.509 -12.923 5.196 1.00 0.00 LIPI
> ATOM 106 H10Y POPE 1 -17.348 -14.376 4.472 1.00 0.00 LIPI
> ATOM 107 C311 POPE 1 -18.588 -12.632 4.746 1.00 0.00 LIPI
> ATOM 108 H11X POPE 1 -19.579 -13.093 4.550 1.00 0.00 LIPI
> ATOM 109 H11Y POPE 1 -18.678 -11.887 5.565 1.00 0.00 LIPI
> ATOM 110 C312 POPE 1 -18.220 -11.803 3.580 1.00 0.00 LIPI
> ATOM 111 H12X POPE 1 -18.892 -10.923 3.487 1.00 0.00 LIPI
> ATOM 112 H12Y POPE 1 -17.220 -11.363 3.783 1.00 0.00 LIPI
> ATOM 113 C313 POPE 1 -18.225 -12.507 2.203 1.00 0.00 LIPI
> ATOM 114 H13X POPE 1 -17.509 -13.356 2.240 1.00 0.00 LIPI
> ATOM 115 H13Y POPE 1 -19.240 -12.936 2.061 1.00 0.00 LIPI
> ATOM 116 C314 POPE 1 -17.884 -11.584 1.011 1.00 0.00 LIPI
> ATOM 117 H14X POPE 1 -16.839 -11.206 1.013 1.00 0.00 LIPI
> ATOM 118 H14Y POPE 1 -18.021 -12.224 0.112 1.00 0.00 LIPI
> ATOM 119 C315 POPE 1 -18.727 -10.322 0.930 1.00 0.00 LIPI
> ATOM 120 H15X POPE 1 -19.752 -10.654 1.201 1.00 0.00 LIPI
> ATOM 121 H15Y POPE 1 -18.404 -9.470 1.565 1.00 0.00 LIPI
> ATOM 122 C316 POPE 1 -18.693 -9.699 -0.511 1.00 0.00 LIPI
> ATOM 123 H16X POPE 1 -18.869 -10.363 -1.384 1.00 0.00 LIPI
> ATOM 124 H16Y POPE 1 -19.343 -8.799 -0.554 1.00 0.00 LIPI
> ATOM 125 H16Z POPE 1 -17.667 -9.344 -0.746 1.00 0.00 LIPI
> ATOM 126 N POPE 2 -16.581 -10.534 24.356 1.00 0.00 11
> ATOM 127 HN1 POPE 2 -16.732 -11.549 24.192 1.00 0.00 11
> ATOM 128 HN2 POPE 2 -16.455 -10.448 25.385 1.00 0.00 11
> ATOM 129 HN3 POPE 2 -17.341 -9.955 23.946 1.00 0.00 11
> ATOM 130 C12 POPE 2 -15.418 -9.959 23.562 1.00 0.00 11
> ATOM 131 H12A POPE 2 -14.494 -10.249 24.107 1.00 0.00 11
> ATOM 132 H12B POPE 2 -15.513 -8.855 23.485 1.00 0.00 11
> ATOM 133 C11 POPE 2 -15.477 -10.490 22.195 1.00 0.00 11
> ATOM 134 H11A POPE 2 -15.479 -11.589 22.357 1.00 0.00 11
> ATOM 135 H11B POPE 2 -16.417 -10.221 21.669 1.00 0.00 11
> ATOM 136 P POPE 2 -13.939 -10.574 20.043 1.00 0.00 11
> ATOM 137 O13 POPE 2 -13.116 -9.584 19.337 1.00 0.00 11
> ATOM 138 O14 POPE 2 -13.410 -11.912 20.205 1.00 0.00 11
> ATOM 139 O11 POPE 2 -15.294 -10.583 19.326 1.00 0.00 11
> ATOM 140 O12 POPE 2 -14.342 -10.006 21.451 1.00 0.00 11
> ATOM 141 C1 POPE 2 -15.777 -11.692 18.643 1.00 0.00 11
> ATOM 142 HA POPE 2 -15.937 -12.530 19.354 1.00 0.00 11
> ATOM 143 HB POPE 2 -16.690 -11.461 18.052 1.00 0.00 11
> ATOM 144 C2 POPE 2 -14.768 -12.202 17.559 1.00 0.00 11
> ATOM 145 HS POPE 2 -13.781 -12.417 18.021 1.00 0.00 11
> ATOM 146 O21 POPE 2 -14.717 -11.182 16.551 1.00 0.00 11
> ATOM 147 C21 POPE 2 -13.685 -11.334 15.740 1.00 0.00 11
> ATOM 148 O22 POPE 2 -12.806 -12.164 15.795 1.00 0.00 11
> ATOM 149 C22 POPE 2 -13.765 -10.175 14.699 1.00 0.00 11
> ATOM 150 H2R POPE 2 -14.793 -9.838 14.445 1.00 0.00 11
> ATOM 151 H2S POPE 2 -13.101 -9.401 15.140 1.00 0.00 11
> ATOM 152 C3 POPE 2 -15.233 -13.539 17.004 1.00 0.00 11
> ATOM 153 HX POPE 2 -14.585 -14.054 16.263 1.00 0.00 11
> ATOM 154 HY POPE 2 -15.065 -14.306 17.790 1.00 0.00 11
> ATOM 155 O31 POPE 2 -16.619 -13.710 16.710 1.00 0.00 11
> ATOM 156 C31 POPE 2 -16.906 -14.067 15.472 1.00 0.00 11
> ATOM 157 O32 POPE 2 -16.145 -14.464 14.651 1.00 0.00 11
> ATOM 158 C32 POPE 2 -18.400 -14.146 15.459 1.00 0.00 11
> ATOM 159 H2X POPE 2 -18.705 -15.059 16.013 1.00 0.00 11
> ATOM 160 H2Y POPE 2 -18.797 -13.189 15.860 1.00 0.00 11
> ATOM 161 C23 POPE 2 -13.208 -10.644 13.348 1.00 0.00 11
> ATOM 162 H3R POPE 2 -13.291 -9.830 12.597 1.00 0.00 11
> ATOM 163 H3S POPE 2 -12.132 -10.897 13.467 1.00 0.00 11
> ATOM 164 C24 POPE 2 -14.021 -11.792 12.774 1.00 0.00 11
> ATOM 165 H4R POPE 2 -14.077 -12.587 13.547 1.00 0.00 11
> ATOM 166 H4S POPE 2 -15.010 -11.289 12.717 1.00 0.00 11
> ATOM 167 C25 POPE 2 -13.478 -12.157 11.411 1.00 0.00 11
> ATOM 168 H5R POPE 2 -12.391 -12.386 11.379 1.00 0.00 11
> ATOM 169 H5S POPE 2 -13.867 -13.135 11.054 1.00 0.00 11
> ATOM 170 C26 POPE 2 -13.814 -11.112 10.310 1.00 0.00 11
> ATOM 171 H6R POPE 2 -13.655 -10.079 10.688 1.00 0.00 11
> ATOM 172 H6S POPE 2 -13.090 -11.358 9.504 1.00 0.00 11
> ATOM 173 C27 POPE 2 -15.266 -10.903 9.760 1.00 0.00 11
> ATOM 174 H7R POPE 2 -15.806 -11.873 9.770 1.00 0.00 11
> ATOM 175 H7S POPE 2 -15.830 -10.494 10.624 1.00 0.00 11
> ATOM 176 C28 POPE 2 -15.386 -9.992 8.529 1.00 0.00 11
> ATOM 177 H8R POPE 2 -16.443 -9.800 8.247 1.00 0.00 11
> ATOM 178 H8S POPE 2 -14.938 -9.003 8.763 1.00 0.00 11
> ATOM 179 C29 POPE 2 -14.678 -10.633 7.334 1.00 0.00 11
> ATOM 180 H91 POPE 2 -15.190 -11.479 6.852 1.00 0.00 11
> ATOM 181 C210 POPE 2 -13.575 -10.196 6.793 1.00 0.00 11
> ATOM 182 H101 POPE 2 -13.240 -10.607 5.829 1.00 0.00 11
> ATOM 183 C211 POPE 2 -12.640 -8.980 7.199 1.00 0.00 11
> ATOM 184 H11R POPE 2 -12.868 -8.683 8.245 1.00 0.00 11
> ATOM 185 H11S POPE 2 -11.579 -9.306 7.163 1.00 0.00 11
> ATOM 186 C212 POPE 2 -12.854 -7.742 6.343 1.00 0.00 11
> ATOM 187 H12R POPE 2 -13.933 -7.479 6.386 1.00 0.00 11
> ATOM 188 H12S POPE 2 -12.174 -6.936 6.692 1.00 0.00 11
> ATOM 189 C213 POPE 2 -12.328 -7.972 4.909 1.00 0.00 11
> ATOM 190 H13R POPE 2 -11.336 -8.463 5.005 1.00 0.00 11
> ATOM 191 H13S POPE 2 -12.985 -8.717 4.410 1.00 0.00 11
> ATOM 192 C214 POPE 2 -12.262 -6.698 4.036 1.00 0.00 11
> ATOM 193 H14R POPE 2 -13.075 -6.009 4.351 1.00 0.00 11
> ATOM 194 H14S POPE 2 -11.355 -6.122 4.318 1.00 0.00 11
> ATOM 195 C215 POPE 2 -12.402 -7.080 2.551 1.00 0.00 11
> ATOM 196 H15R POPE 2 -11.731 -7.924 2.282 1.00 0.00 11
> ATOM 197 H15S POPE 2 -13.468 -7.305 2.335 1.00 0.00 11
> ATOM 198 C216 POPE 2 -12.163 -5.875 1.636 1.00 0.00 11
> ATOM 199 H16R POPE 2 -12.918 -5.077 1.804 1.00 0.00 11
> ATOM 200 H16S POPE 2 -11.147 -5.477 1.843 1.00 0.00 11
> ATOM 201 C217 POPE 2 -12.156 -6.088 0.154 1.00 0.00 11
> ATOM 202 H17R POPE 2 -11.427 -6.895 -0.073 1.00 0.00 11
> ATOM 203 H17S POPE 2 -13.164 -6.398 -0.194 1.00 0.00 11
> ATOM 204 C218 POPE 2 -11.667 -4.984 -0.769 1.00 0.00 11
> ATOM 205 H18R POPE 2 -10.615 -4.687 -0.572 1.00 0.00 11
> ATOM 206 H18S POPE 2 -11.858 -5.307 -1.815 1.00 0.00 11
> ATOM 207 H18T POPE 2 -12.274 -4.060 -0.660 1.00 0.00 11
> ATOM 208 C33 POPE 2 -18.924 -14.271 14.060 1.00 0.00 11
> ATOM 209 H3X POPE 2 -18.718 -15.246 13.570 1.00 0.00 11
> ATOM 210 H3Y POPE 2 -20.020 -14.362 14.219 1.00 0.00 11
> ATOM 211 C34 POPE 2 -18.653 -13.077 13.218 1.00 0.00 11
> ATOM 212 H4X POPE 2 -18.670 -12.145 13.824 1.00 0.00 11
> ATOM 213 H4Y POPE 2 -17.636 -13.194 12.787 1.00 0.00 11
> ATOM 214 C35 POPE 2 -19.632 -12.861 12.028 1.00 0.00 11
> ATOM 215 H5X POPE 2 -19.847 -13.760 11.411 1.00 0.00 11
> ATOM 216 H5Y POPE 2 -20.630 -12.537 12.392 1.00 0.00 11
> ATOM 217 C36 POPE 2 -19.197 -11.799 11.007 1.00 0.00 11
> ATOM 218 H6X POPE 2 -18.855 -10.943 11.626 1.00 0.00 11
> ATOM 219 H6Y POPE 2 -18.352 -12.353 10.546 1.00 0.00 11
> ATOM 220 C37 POPE 2 -20.284 -11.350 9.991 1.00 0.00 11
> ATOM 221 H7X POPE 2 -20.676 -12.197 9.387 1.00 0.00 11
> ATOM 222 H7Y POPE 2 -21.090 -10.803 10.525 1.00 0.00 11
> ATOM 223 C38 POPE 2 -19.519 -10.496 8.945 1.00 0.00 11
> ATOM 224 H8X POPE 2 -19.143 -9.581 9.452 1.00 0.00 11
> ATOM 225 H8Y POPE 2 -18.575 -11.029 8.701 1.00 0.00 11
> ATOM 226 C39 POPE 2 -20.343 -9.998 7.741 1.00 0.00 11
> ATOM 227 H9X POPE 2 -20.563 -10.858 7.073 1.00 0.00 11
> ATOM 228 H9Y POPE 2 -21.382 -9.715 8.012 1.00 0.00 11
> ATOM 229 C310 POPE 2 -19.744 -8.789 7.060 1.00 0.00 11
> ATOM 230 H10X POPE 2 -19.851 -7.979 7.814 1.00 0.00 11
> ATOM 231 H10Y POPE 2 -18.663 -9.003 6.920 1.00 0.00 11
> ATOM 232 C311 POPE 2 -20.500 -8.346 5.840 1.00 0.00 11
> ATOM 233 H11X POPE 2 -20.709 -9.171 5.126 1.00 0.00 11
> ATOM 234 H11Y POPE 2 -21.475 -7.934 6.180 1.00 0.00 11
> ATOM 235 C312 POPE 2 -19.817 -7.197 5.026 1.00 0.00 11
> ATOM 236 H12X POPE 2 -20.466 -6.802 4.215 1.00 0.00 11
> ATOM 237 H12Y POPE 2 -19.488 -6.300 5.593 1.00 0.00 11
> ATOM 238 C313 POPE 2 -18.536 -7.654 4.332 1.00 0.00 11
> ATOM 239 H13X POPE 2 -17.691 -7.842 5.027 1.00 0.00 11
> ATOM 240 H13Y POPE 2 -18.741 -8.676 3.948 1.00 0.00 11
> ATOM 241 C314 POPE 2 -18.015 -6.856 3.191 1.00 0.00 11
> ATOM 242 H14X POPE 2 -18.660 -6.829 2.288 1.00 0.00 11
> ATOM 243 H14Y POPE 2 -17.997 -5.799 3.532 1.00 0.00 11
> ATOM 244 C315 POPE 2 -16.608 -7.353 2.722 1.00 0.00 11
> ATOM 245 H15X POPE 2 -15.904 -7.207 3.569 1.00 0.00 11
> ATOM 246 H15Y POPE 2 -16.827 -8.417 2.490 1.00 0.00 11
> ATOM 247 C316 POPE 2 -16.157 -6.467 1.545 1.00 0.00 11
> ATOM 248 H16X POPE 2 -15.282 -6.911 1.025 1.00 0.00 11
> ATOM 249 H16Y POPE 2 -17.122 -6.400 0.998 1.00 0.00 11
> ATOM 250 H16Z POPE 2 -15.893 -5.459 1.932 1.00 0.00 11
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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