[gmx-users] Incorrectly added water molecule by genbox.

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 3 09:55:27 CEST 2014

On Thu, Jul 3, 2014 at 9:17 AM, Dawid das <addiw7 at googlemail.com> wrote:

> Hi,
> I have a following issue. Genbox seems to add a water molecule inside small
> protein cavity and it does not belong there. Can I manually remove it from
> *gro file?

Yes, but you need to make a matching change to the [molecules] section of
any matching .top file.

> What with the numbering of residues in this situation?

Immaterial. The only important thing in such cases is that there is a
change; the values or the delta-value is not noticed.


> The
> problem is that this water molecule can't be settled during minimization
> and it spoils everything.
> Dawid
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