[gmx-users] numbering after 99999SOL

[gromacs query]

>> Gromacs do not use residue number or atom number,

OK! Thanks Nuno and Mark

regards,


On Tue, May 14, 2013 at 7:14 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Try selecting residue 0 with editconf and see for yourself :-)
> On May 14, 2013 4:41 PM, "gromacs query" <gromacsquery at gmail.com> wrote:
>
> > Dear Nuno,
> >
> > I used genconf -f del.gro -o del.g96
> >
> > Again it gives max of 99999 then starts with 0; sample shown here
> >
> > del.g96
> >
> > 99999 SOL   OW    332114   13.572999954    1.925999999   13.545999527
> > 99999 SOL   HW1   332115   13.491999626    1.927000046   13.604000092
> > 99999 SOL   HW2   332116   13.576000214    2.009000063   13.491000175
> >     0 SOL   OW    332117   14.468000412    3.049999952   13.074999809
> >     0 SOL   HW1   332118   14.500000000    2.973999977   13.131999969
> >     0 SOL   HW2   332119   14.376000404    3.076999903   13.104999542
> >
> >
> > I am just wondering if I need to select some residue for analysis, say
> 0SOL
> > then it will see two 0SOL (one real 0SOL and one repeated after
> 99999SOL).
> > Here its just water that may not need analysis in particular but for huge
> > membrane or proteins or polymers how this analysis will be handled.
> > regards,
> >
> >
> >
> > On Tue, May 14, 2013 at 5:22 PM, Nuno Azoia <nazoia at gmail.com> wrote:
> >
> > > I'm guessing that you are using .gro file format.
> > > That's a limitation of the file format. See
> > > http://manual.gromacs.org/online/gro.html
> > >
> > > If you really need different residue number for each residue, use .g96
> > file
> > > format instead.
> > >
> > > Cheers
> > >
> > > Nuno Azoia
> > >
> > >
> > > On Tue, May 14, 2013 at 3:08 PM, gromacs query <gromacsquery at gmail.com
> > > >wrote:
> > >
> > > > Dear All,
> > > >
> > > > I have a huge system and residue number goes beyond 99999. So when I
> > > added
> > > > waters then residue number goes till 99999SOL then again it starts
> from
> > > > 0SOL. I tried genconf -renumber option but it does not help.
> > > >
> > > > Though it can be done with small scripting, just want to know if it
> can
> > > be
> > > > done with Gromacs.
> > > >
> > > > regards,
> > > > JIom
> > > > --
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> > >
> > >
> > > --
> > > Nuno Gonçalo Azoia Lopes
> > >
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