[gmx-users] atom type not found error
spoel at xray.bmc.uu.se
Tue Dec 16 20:17:01 CET 2003
On Tue, 2003-12-16 at 19:46, Yu Sun (Denis) wrote:
> My pdb file is not a protein but a polymer surface I modeled. However,
> when I checked with the tutorial examples, with speptide.pdb same error
> message occurred. In the case of speptide.pdb, if I choose forecefiled 1,
> It is fine.
polymers won't work in pdb2gmx (unless they're proteins). you'll have to
generate a topology yourself.
> At 06:22 PM 12/16/2003 +0100, Ruben Martinez Buey wrote:
> >Hi Yu Sun,
> >Probably, your pdb file contains heteroatoms or has a strange nomenclature
> >that GROMACS cannot recognice.
> >Have you checked this?
> >Hope this help
> >good luck!
> >Yu Sun (Denis) wrote:
> >>Dear Gmx usrs,
> >>When using pdb2gmx, selected forcefield 0, got fatal error:
> >>Atom type N(residue ABU) not found in atomtype database
> >>Could someone kindly explain to me how to fix this problem ?
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David van der Spoel, PhD, Assist. 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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