[gmx-users] missing atom

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 23 13:07:16 CEST 2004

On Wed, 2004-06-23 at 12:55, herbst at fhi-berlin.mpg.de wrote:
> 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 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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