[gmx-users] How the topology file is created based on *.gro file?

[Diogo Vila Viçosa]

If you still need to correct your numbering (for scripting porposes for
example) you can convert your original.gro using editconf and in the final
gro file will be corrected.

On Wed, Feb 3, 2016 at 11:24 AM Dawid das <addiw7 at googlemail.com> wrote:

> So it turns out that what is important is the order, i.e. when I want
> connection
> between residues 164 and 165 they need to go in order in my *gro file.
> Otherwise there
> won't be any bonding in the topology.
>
> Best wishes,
> Dawid Grabarek
>
> 2016-02-03 10:29 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > Atom numbering is unimportant, but you might see warnings from tools that
> > recognise it is weird. Residue numbering is important only in that the
> > value changes when the residue does - it doesn't have to go up by one.
> Try
> > it and see ;-)
> >
> > Mark
> >
> > On Wed, 3 Feb 2016 10:13 Dawid das <addiw7 at googlemail.com> wrote:
> >
> > > Dear Gromacs Experts,
> > >
> > > Let's assume that I have a *.gro file in a proper format but the number
> > of
> > > atoms and/or
> > > residues is let's say random, e.g. I have coordinates of atoms for
> > residue
> > > 87, 95, 96, 88.
> > > What is more, I have let's say 76 atoms in the system, but I start
> > > numbering from 999.
> > > Will I be able to produce proper *.top file if the definition of atoms
> > and
> > > their parameters
> > > is correct?
> > >
> > > Best wishes,
> > > Dawid Grabarek
> > > --
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