[gmx-users] Re: Re: GENION: Ions inside the protein (Viswanadham Sridhara & Tsjerk Wassenaar)

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 12 08:47:36 CEST 2006

Hi Una,

That seems perfectly sensible. The only thing is that I'd use editconf
for renumbering, but I'm not even sure whether that will actually make
a difference.



On 10/11/06, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> Thank you so much for your response Viswanadham Sridhara and Tsjerk
> Wassenaar Still I seem to be doing something wrong because the ions
> always end up in the active site cleft!. This is what I do: 1. I move
> the 2 watermolecules (all three atoms) which I don't want to be replaced
> at the bottom of the .gro file generated from genbox 2. Than I make
> another .gro file using genconf to renumber the atoms 3. Make a .ndx
> file from the renumbered .gro file and than delete the last 6 atoms from
> the [SOL] group 4. Run genion after grompp using the .ndx file and
> choose group [SOL] and a new .gro file is generated If you could comment
> on this than that would be highly appreaciated. Best regards, Una 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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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

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