[gmx-users] A common error Atom O11 in residue bDM 1 was not found in rtp entry

Justin A. Lemkul jalemkul at vt.edu
Sat Sep 25 22:02:55 CEST 2010



ABEL Stephane 175950 wrote:
> Dear all, 
>  
> I have a very "common" problem when I try to convert a pdb file to a gro file with the following command.
>  
> I use charmm27ff and gmx4.5.1.
>  
> pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp
>  
> I obtain the following "commun" error :
>  
> "Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms while sorting atoms". 
>  
> I am surprised to have this message, since after verification in the 1-bDM.pdb, I have not found an atom with this name. I have also checked the format of the pdb and all the fields are in right place. 
>  

Probably atom 1O1 is being translated as O11.  I have had similar problems with 
translated atom names.  If you add "-debug 1" to your pdb2gmx command line, you 
will get output .pdb files containing the structure as pdb2gmx is interpreting 
it.  That's how I've identified some spurious translations before.

-Justin

> Below my PDB file
> ATOM      1 1C1  bDM     1     -28.807  -8.973  -4.361  0.30  0.00
> ATOM      2 H1A  bDM     1     -28.976  -9.551  -3.427  0.10  0.00
> ATOM      3 1O1  bDM     1     -27.541  -9.232  -4.796 -0.40  0.00
> ATOM      4 1C2  bDM     1     -29.836  -9.352  -5.325  0.14  0.00
> ATOM      5 H2A  bDM     1     -30.783  -9.324  -4.746  0.09  0.00
> ATOM      6 1O2  bDM     1     -29.680 -10.694  -5.733 -0.66  0.00
> ATOM      7 H2OA bDM     1     -28.731 -10.800  -5.827  0.43  0.00
> ATOM      8 1C3  bDM     1     -29.990  -8.385  -6.493  0.14  0.00
> ATOM      9 H3A  bDM     1     -29.086  -8.411  -7.139  0.09  0.00
> ATOM     10 1O3  bDM     1     -31.239  -8.585  -7.237 -0.66  0.00
> ATOM     11 H3OA bDM     1     -31.193  -8.053  -8.035  0.43  0.00
> ATOM     12 1C4  bDM     1     -29.957  -6.922  -6.018  0.14  0.00
> ATOM     13 H4A  bDM     1     -30.923  -6.772  -5.490  0.09  0.00
> ATOM     14 1O4  bDM     1     -29.963  -6.003  -7.122 -0.66  0.00
> ATOM     15 H4OA bDM     1     -29.993  -5.118  -6.751  0.43  0.00
> ATOM     16 1C5  bDM     1     -28.865  -6.650  -5.081  0.10  0.00
> ATOM     17 H5A  bDM     1     -27.963  -7.009  -5.622  0.10  0.00
> ATOM     18 1C6  bDM     1     -28.730  -5.254  -4.552  0.05  0.00
> ATOM     19 H61A bDM     1     -29.694  -5.009  -4.056  0.09  0.00
> ATOM     20 H61B bDM     1     -28.509  -4.622  -5.438  0.09  0.00
> ATOM     21 1O6  bDM     1     -27.593  -5.254  -3.684 -0.66  0.00
> ATOM     22 H6OA bDM     1     -27.699  -5.900  -2.982  0.43  0.00
> ATOM     23 1O5  bDM     1     -28.979  -7.582  -3.963 -0.40  0.00
> ATOM     24 2C1  bDM     1     -23.620  -9.286  -3.000  0.20  0.00
> ATOM     25 H1B  bDM     1     -23.440 -10.274  -3.475  0.09  0.00
> ATOM     26 2C2  bDM     1     -24.806  -9.283  -2.026  0.14  0.00
> ATOM     27 H2B  bDM     1     -24.867  -8.235  -1.662  0.09  0.00
> ATOM     28 2O2  bDM     1     -24.477 -10.097  -0.884 -0.66  0.00
> ATOM     29 H2OB bDM     1     -23.792  -9.775  -0.294  0.43  0.00
> ATOM     30 2C3  bDM     1     -26.163  -9.642  -2.661  0.14  0.00
> ATOM     31 H3B  bDM     1     -26.142 -10.663  -3.098  0.09  0.00
> ATOM     32 2O3  bDM     1     -27.232  -9.397  -1.722 -0.66  0.00
> ATOM     33 H3OB bDM     1     -27.384 -10.156  -1.155  0.43  0.00
> ATOM     34 2C4  bDM     1     -26.364  -8.872  -3.987  0.10  0.00
> ATOM     35 H4B  bDM     1     -26.533  -7.835  -3.626  0.10  0.00
> ATOM     36 2C5  bDM     1     -25.089  -8.936  -4.892  0.25  0.00
> ATOM     37 H5B  bDM     1     -24.906  -9.942  -5.326  0.09  0.00
> ATOM     38 2C6  bDM     1     -25.225  -7.980  -6.074  0.05  0.00
> ATOM     39 H62A bDM     1     -25.159  -6.910  -5.780  0.09  0.00
> ATOM     40 H62B bDM     1     -26.236  -8.045  -6.532  0.09  0.00
> ATOM     41 2O5  bDM     1     -24.218  -8.289  -7.105 -0.66  0.00
> ATOM     42 H5OB bDM     1     -24.661  -8.895  -7.704  0.43  0.00
> ATOM     43 2O4  bDM     1     -24.011  -8.432  -4.077 -0.40  0.00
> ATOM     44 2O1  bDM     1     -22.364  -8.895  -2.386 -0.30  0.00
> ATOM     45 C7   bDM     1     -21.159  -9.105  -3.148 -0.11  0.00
> ATOM     46 H7A  bDM     1     -20.922 -10.188  -3.228  0.09  0.00
> ATOM     47 H7B  bDM     1     -21.320  -8.848  -4.217  0.09  0.00
> ATOM     48 C8   bDM     1     -19.961  -8.389  -2.410 -0.18  0.00
> ATOM     49 H8A  bDM     1     -19.829  -8.778  -1.378  0.09  0.00
> ATOM     50 H8B  bDM     1     -20.171  -7.300  -2.464  0.09  0.00
> ATOM     51 C9   bDM     1     -18.547  -8.641  -3.005 -0.18  0.00
> ATOM     52 H9A  bDM     1     -18.718  -8.465  -4.089  0.09  0.00
> ATOM     53 H9B  bDM     1     -18.415  -9.744  -3.010  0.09  0.00
> ATOM     54 C10  bDM     1     -17.452  -7.785  -2.397 -0.18  0.00
> ATOM     55 H10A bDM     1     -16.675  -7.915  -3.180  0.09  0.00
> ATOM     56 H10B bDM     1     -17.700  -6.702  -2.407  0.09  0.00
> ATOM     57 C11  bDM     1     -16.987  -8.238  -1.043 -0.18  0.00
> ATOM     58 H11A bDM     1     -16.658  -9.299  -1.039  0.09  0.00
> ATOM     59 H11B bDM     1     -17.874  -8.295  -0.376  0.09  0.00
> ATOM     60 C12  bDM     1     -15.798  -7.399  -0.595 -0.18  0.00
> ATOM     61 H12A bDM     1     -16.131  -6.343  -0.678  0.09  0.00
> ATOM     62 H12B bDM     1     -14.966  -7.559  -1.314  0.09  0.00
> ATOM     63 C13  bDM     1     -15.271  -7.639   0.808 -0.18  0.00
> ATOM     64 H13A bDM     1     -15.139  -8.740   0.874  0.09  0.00
> ATOM     65 H13B bDM     1     -15.946  -7.348   1.641  0.09  0.00
> ATOM     66 C14  bDM     1     -13.783  -7.068   1.047 -0.18  0.00
> ATOM     67 H14A bDM     1     -13.635  -7.658   1.976  0.09  0.00
> ATOM     68 H14B bDM     1     -13.020  -7.442   0.331  0.09  0.00
> ATOM     69 C15  bDM     1     -13.644  -5.563   1.231 -0.18  0.00
> ATOM     70 H15A bDM     1     -14.224  -5.173   2.096  0.09  0.00
> ATOM     71 H15B bDM     1     -14.037  -5.111   0.296  0.09  0.00
> ATOM     72 C16  bDM     1     -12.181  -5.162   1.586 -0.18  0.00
> ATOM     73 H16A bDM     1     -12.171  -4.210   2.159  0.09  0.00
> ATOM     74 H16B bDM     1     -11.783  -5.869   2.345  0.09  0.00
> ATOM     75 C17  bDM     1     -11.148  -4.862   0.380 -0.18  0.00
> ATOM     76 H17A bDM     1     -10.974  -5.725  -0.298  0.09  0.00
> ATOM     77 H17B bDM     1     -11.602  -4.094  -0.283  0.09  0.00
> ATOM     78 C18  bDM     1      -9.916  -4.271   0.993 -0.27  0.00
> ATOM     79 H18A bDM     1     -10.161  -3.350   1.564  0.09  0.00
> ATOM     80 H18B bDM     1      -9.245  -3.989   0.153  0.09  0.00
> ATOM     81 H18C bDM     1      -9.391  -4.974   1.675  0.09  0.00
> Any help will be appreciated !
> Stefane

-- 
========================================

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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