[gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 29 13:29:15 CEST 2011
Leonhard Henkes wrote:
> 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.
>
The only species you have to explicitly deal with are the protein and lipids.
The water and ions do not need to be processed by pdb2gmx. Their topologies are
handled by #include statements later.
> 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.
The combination of long bond warnings and mismatching names suggests that the
.pdb file is misformatted. Gromacs requires that the exact PDB standard be
upheld, and a quick look at your file indicates that at the very least, your
coordinate columns are shifted left, which leads to incorrect interpretation of
the values and gives the long bond warnings. This may also have a side effect
related to the atom names. Start over with a correctly formatted .pdb file.
-Justin
> 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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
--
========================================
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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