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

[Justin Lemkul]

On 12/10/19 2:15 AM, 변진영 wrote:
> Thank you Sir,. I found the typo in my topol.top file.
> So I changed the 'InflatGRO' to 'InflateGRO' and prompted the grompp module.
> However I have got the new error:
>
> Fatal error:
> number of coordinates in coordinate file (system_inflated.gro, 6538)
>               does not match topology (topol.top, 138)
>
> I might know why both the coordinate file (system_inflated.gro) and
> topology file(topol.top) have the same number of coordinates.
> But in tutorial the system_inflated.gro file is produced by concatenating
> the KALP_newbox.gro file and dppc128_whole.gro file, so it's no wonder that
> the number of coordinates in system_inflated.gro file is different with the
> number of coordinates in topol.top file which is produced by prompting the
> gmx pdb2gmx module.
>
> I don' t know what I missed.. Any idea as to what cause this problem?

You have to update the topology after adding DPPC. Follow the tutorial 
exactly; it tells you this.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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