[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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