[gmx-users] peptide-membrane simulations

maite lopez lopezmai at gmail.com
Thu Mar 15 13:48:12 CET 2007

Hi Justin :

how Tsjerk said me yesterday i forgot to change the number of the
atoms in the .gro file. Now i don't have this error when i run
editconfig command.



On 3/14/07, Justin Lemkul <jalemkul at vt.edu> wrote:

> > Fatal error:
> > Invalid line in peptide_dppc64_water.gro for atom 20704:
> >    4.72500   4.23200  12.00000
> >
> This looks like a box dimension line.  Have you renumbered the .gro file?  The
> second line in the .gro file specifies the number of atoms in the file, and if
> you have manually deleted water molecules, the number of atoms in the system
> will be less than what you started with.
> At least, that's been my experience when dealing with similar systems.
> -Justin
> Justin A. Lemkul
> Biochemistry
> Alpha Chi Sigma, AI '04
> Virginia Tech
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