[gmx-users] GENION: Ions inside the protein

[Tsjerk Wassenaar]

Hi,

The error message tries to make clear that genion can only replace
water molecules in an index group without gaps. It has to be
continuous. So the point that was made earlier on the list was that
the water molecules should be deleted in the .gro file. Alternatively,
they can also be moved to the beginning of the end of the solvent
section and from the (renumbered) resulting file an index file can be
constructed.

Hope it helps,

Tsjerk

On 10/10/06, Viswanadham Sridhara <muta.mestri at gmail.com> wrote:
> you might have deleted just one atom of water molecule.
> Ex: If you are using SPC water , you have to delete all 3 atoms in index
> file.
>
>
> Best way is to make changes in .gro file..
> Renumber the resulting .gro file using genconf, make a new index file and
> start running.
>
>
>
> On 10/10/06, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> > Dear users,
> >
> > In some of my simulations after neutralizing the systems with genion 2
> > of the ions were inside the active site cleft of the protein.
> > In the discussion on the list it was commented to either delete the
> > solvent within the protein which I did I deleted the water molecule
> > (11798) and gave genion that index file as input but than this error came:
> >
> > Fatal error: The solvent group is not continuous: index[8198]=11797,
> > index[8199]=11799
> >
> > I don't want to use the -random command in genion if possible because in
> > none of the other simulations I have used it.
> >
> > Is there any other way to delete the solvent within the protein did I
> > misunderstand that so those water molecules will not be replaced?
> >
> > Best regards, Una Bjarnadottir
> >
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>
>
> --
> Viswanadham Sridhara,
> Research Assistant,
> Old Dominion University,
> Norfolk, Va-23529.
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336