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

[Mark Abraham]

Hi,

These things can all be handled by pdb2gmx chain-separation (which
regulates whether the topology generator will expect to make bonds between
residues adjacent in the sequence in the input file) and merging machinery
(if you want your cutout region to be all in the same [moleculetype] or
not), based on either PDB chain ID, TER records or both. See gmx pdb2gmx -h.

Mark

On Wed, Feb 3, 2016 at 12:42 PM Dawid das <addiw7 at googlemail.com> wrote:

> 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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