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

[Dawid das]

Okay, now when I did some tests I can explain more precisely what I want to
do.

As I wrote in my other message, I have to cut out some of the amino acids
from my protein.
They are supposed to create an environment around the central amino acid
residue (chromophore in my case).
Because the peptide bonds were cleaved I want to cap them with methyl
groups. I start from *.gro file
with results from MD trajectory.

So I cut out the environment, let's say residues 34, 55-56-57 and 89 from
my original *.gro file
and create new cut-out.gro file. Now I need those methyl groups to cap both
ends of residues 34 and 89
, the N-end of residue 55 and C-end of residue 57. So the order of residues
in my cut-out.gro file
must be like:
100
34
101
102
55
56
57
103
104
89
105

I used 100-105 for methyl "residues" (I guess I will manage to define them
as I have already done this kind
of stuff) numbering because this number does not matter. It's just an
example.
So now my question is won't pdb2gmx create bonds between 101 -  102
residues or 103-104?
I don't want that obviously.

And one more thing. Is it possible to create proper bonds when the order of
my residues is like:
34
55
56
57
89
100
101
.
.
.

so no bond between 34 - 55 but bonds between 100 - 34 - 101 , 102 - 55 and
so on?

Best wishes,
Dawid Grabarek

2016-02-03 12:29 GMT+01:00 Diogo Vila Viçosa <diogo.vicosa at fc.ul.pt>:

> 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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