[gmx-users] numbering after 99999SOL

[Mark Abraham]

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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> >
> >
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