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

Arindam Ganguly arindamganguly at gmail.com
Thu Mar 9 20:11:51 CET 2006

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

VILLIN in water
    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
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