[gmx-users] Error: Atoms in the .top are not numbered consecutively

[Justin Lemkul]

On 12/3/19 9:31 PM, 변진영 wrote:
> Dear All,
>
> I am gromacs beginner and I have gone through the Justing Lemku tutorial
> for KALP_15 in DPPC.
> I have reach the step three and trying to solve the error.
> The command line is:
>    $ gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top
> -r system_inflated.gro -o system_inflated_em.tpr
>
> And the error message is:
>    ERROR 1 [file topol.top, line 31]:
>    Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
>    1, while at->nr = 50)
>
> So I check the topol.top file and think that there is no problem in
> topol.top file
> Is there anything I lost when I prompted the grompp module? I don' t know
> what I missed..
>
> Any idea as to what cause this problem?

This suggests a syntax problem, perhaps introduced by typos or incorrect 
positioning of #include statements.

-Justin

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Justin A. Lemkul, Ph.D.
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