[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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