[gmx-users] topology error

[David]

On Fri, 2004-09-17 at 22:08, parinald at unsl.edu.ar wrote:
> Thans`s David and Patricia:
>                            I check the topology very times carefully
> but the error message is the same;
> 
> #define _FF_GROMOS96
> #define _FF_GROMOS96A
> 
>   [defaults]
> 1    1    no    1.0    1.0
>   ..........
>   ..........
> ;new start the molecular definitions
>   [moleculetype]
>   [atoms]
>   [bonds]
>   [pairs]
>   [angles]
>   [dihedrals]
>   [dihedrals]
> #include "dmso.itp"
>   [system]
> Protein
>   [molecules]
> Protein      1
> DMSO       3579
> 
>                      there is any way to look out how gromacs read the
> topology file?. Somebody has worked out with convert
> topology?

I don't know how the convert script works, but you can see what grompp
makes of it by running grompp -debug and checking the grompp.log file.

>                Thank`s again.
> 
> 
> > 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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> >> http://www.gromacs.org/mailman/listinfo/gmx-users
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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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> > gmx-users at gromacs.org
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> >
> 
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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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