[gmx-users] atom type not found error

[David]

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.

> 
> Thanks,
> 
> Denis
> 
> 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!
> >
> >Ruebn
> >
> >
> >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 ?
> >>
> >>Thanks,
> >>
> >>Denis
> >>
> >>_______________________________________________
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++