[gmx-users] Villin Benchmarks grompp error (Please Help)

[Daniela S. Mueller]

hi arindam,

run pdb2gmx first to generate a topology-file. it would contain a bit
more than yours...

best regards, 
daniela


On Thu, 2006-03-09 at 13:11 -0600, Arindam Ganguly wrote:
> Hi GROMACS users,
> sorry please disregard the earlier message realised it was too long.
> i am new to GROMACS. i have been trying to run the Villin Benchmarks
> using the conf.gro, grompp.mdp and topol.top file provided with the
> benchmark folder. i giving the grompp command as follows 
> 
> grompp -f grompp.mdp -c conf.pdb -p topol.top -o em.tpr
> 
> and after that i get this message,
> 
> Fatal error:
> number of coordinates in coordinate file (conf.pdb , 9389)
>              does not match topology (topol.top, 0)
> -------------------------------------------------------
> 
> "The Candlelight Was Just Right" (Beastie Boys) 
> 
> After going through the GROMACS mailing list I realised this is a
> classical mistake which everyone makes. that's fine, but even after
> making the changes as pointed out by many users that check the number
> of atoms in topol.top and conf.gro file i am still getting the same
> error.
> i am providing in the email conf.gro and the topol.top file. can
> anyone of you plz suggest as to what is wrong. where i have to make
> the changes
> inorder for me to run the simulation.thanks.
> the file are provided below.
> 
> Arindam Ganguly
> 
> conf.gro
> VILLIN in water
>  9389
>     1MET      N    1   2.185   2.903   2.012 -0.4460 -0.1439  0.3043
> last line of the conf.gro file
> 3036SOL    HW2 9389   4.069   1.007   3.359  0.8423 -0.6670 -0.9379
>    5.02729   4.73973   4.10445   0.00000   0.00000   1.67574   0.00000
> -1.67574   2.36986
> 
> topol.top file
> [ system ]
> ; Name
> VILLIN in water
> 
> [ molecules ]
> ; Compound        #mols
> Protein           390
> SOL              8999
> 
> 
> 

-- 

Daniela S. Mueller

biologist (Diplom, German degree)
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