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

[Dawid das]

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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