[gmx-users] topology error

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 17 08:55:59 CEST 2004

On Fri, 2004-09-17 at 00:06, parinald at unsl.edu.ar wrote:
> Hi All:
>        I have a non-protein molecule in DMSO.
> After convert gromos96 topology file to Gromacs topology (with convert
> program), I try to execute grompp...
> processing topology...
> Generated 0 of the 946 non-bonded parameter combinations
> Cleaning up temporary file grompp9xctdT
> Fatal error: Moleculetype Protein contains no atoms
you'll have to check the .top file with chapter 5 of the manual close
by. There definitely is an error in the topology but it's impossible to
judge what. Maybe missing [ atoms ] section?
> I don`t know how to avoid (or solve) this problem, any idea?
>                                               Thank you very very much.
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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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