[gmx-users] missing atom

[herbst at fhi-berlin.mpg.de]

So I should call it O instead of O1 in the rtp-file? What if I have
another oxygen in the molecule? Call it O as well? CYL is a spinlabeled
sidechain added to the protein for EPR-Experiments.

>> Hello all,
>> when I create my .top file from my .pdb file with pdb2gmx, the following
>> warning appears:
>>
>> WARNING: atom O1 is missing in residue CYL 75 in the pdb file
>>
>> But the atom is definitely there, I can see it when I look at the
>> pdb-file
>> with a graphic program, and it also has the right name. So why does
>> pdb2gmx not recognize it?
> it is renamed to O.
> check xlateat.dat
> this is necessary for termini. what is CYL by the way?
>>
>> Thanks,
>> Anna
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone:  +46 18 471 4205  fax: +46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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