[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27
Leonhard Henkes
Kalavera at gmx.net
Wed Jun 29 12:00:21 CEST 2011
Thanks for your reply,
my whole pdb file includes an equilibrated membrane bilayer, constructed with VMD for NAMD. I used the CHARMM27 FF while constructing it.
Now, I wanted to convert this system for a run in Gromacs.
To solve my issus, I divided my system into four new pdb's (ion, water, lipids, protein). This was an advise I found in an older thread. In the end, all created *.gro files will be united again, to one big file.
I checked the POPE entry in the charmff folder and the lipid names are the same as in my pdb. So I assumed that my bilayer can be converted with pdb2gmx too. The occurring errors are attached.
I don't understand these errors.
Thanks for your help,
M.Kalavera
...
Warning: Long Bond (232-234 = 0.547183 nm)
Warning: Long Bond (232-235 = 0.710465 nm)
Warning: Long Bond (235-236 = 0.514028 nm)
Warning: Long Bond (235-237 = 0.707876 nm)
Warning: Long Bond (235-238 = 0.341151 nm)
Warning: Long Bond (238-239 = 0.545028 nm)
Warning: Long Bond (238-240 = 0.538926 nm)
Warning: Long Bond (241-242 = 0.586707 nm)
Warning: Long Bond (241-243 = 0.360561 nm)
Warning: Long Bond (241-244 = 0.447081 nm)
Warning: Long Bond (244-245 = 0.57 nm)
Warning: Long Bond (244-246 = 0.412897 nm)
Warning: Long Bond (244-247 = 0.414759 nm)
Warning: Long Bond (247-248 = 0.785856 nm)
Warning: Long Bond (247-249 = 0.865684 nm)
Warning: Long Bond (247-250 = 0.447969 nm)
WARNING: atom P is missing in residue POPE 1 in the pdb file
WARNING: atom O13 is missing in residue POPE 1 in the pdb file
WARNING: atom O14 is missing in residue POPE 1 in the pdb file
WARNING: atom O11 is missing in residue POPE 1 in the pdb file
WARNING: atom O12 is missing in residue POPE 1 in the pdb file
WARNING: atom C1 is missing in residue POPE 1 in the pdb file
WARNING: atom HA is missing in residue POPE 1 in the pdb file
You might need to add atom HA to the hydrogen database of building block POPE
in the file lipids.hdb (see the manual)
WARNING: atom HB is missing in residue POPE 1 in the pdb file
You might need to add atom HB to the hydrogen database of building block POPE
in the file lipids.hdb (see the manual)
WARNING: atom C2 is missing in residue POPE 1 in the pdb file
WARNING: atom HS is missing in residue POPE 1 in the pdb file
You might need to add atom HS to the hydrogen database of building block POPE
in the file lipids.hdb (see the manual)
WARNING: atom O21 is missing in residue POPE 1 in the pdb file
WARNING: atom C21 is missing in residue POPE 1 in the pdb file
WARNING: atom O22 is missing in residue POPE 1 in the pdb file
WARNING: atom C22 is missing in residue POPE 1 in the pdb file
WARNING: atom H2R is missing in residue POPE 1 in the pdb file
You might need to add atom H2R to the hydrogen database of building block POPE
in the file lipids.hdb (see the manual)
WARNING: atom H2S is missing in residue POPE 1 in the pdb file
You might need to add atom H2S to the hydrogen database of building block POPE
in the file lipids.hdb (see the manual)
WARNING: atom C3 is missing in residue POPE 1 in the pdb file
...
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 4.5.4
Source code file: /usr/people/../gromacs-4.5.4/src/kernel/pdb2top.c, line: 1463
Fatal error:
There were 250 missing atoms in molecule Lipids, if you want to use this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
>
>
> 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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