[gmx-users] Water naming

[Mark Abraham]

Hi,

Probably because of this exact issue, GROMACS tools generally pay no
attention to the numbering of atoms and residues in coordinate files,
except to notice when those numbers change. The internal counters are
unrelated to the numbers in the file. So you can safely index residue
20000, etc. Try it with something simple and see for yourself! :-)

Mark


On Thu, Feb 13, 2014 at 12:10 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Dear Sir,
>
> For extracting specific waters involved in Hbond from the pdb I am using
> a small script wherein i have to use the only information given in the
> index
> file, generated from g_hbond, that is the atom number. so I am not clear
> with it even now. Also the same problem is there with the residue numbering
> of SOL in the, maximum is 9999 and the it restarts with 0.
>
> I still did not get your suggestion sir, please excuse my ignorance.
>
> Regards
> kavya
>
>
> On Thu, Feb 13, 2014 at 3:33 PM, Erik Marklund
> <erik.marklund at chem.ox.ac.uk>wrote:
>
> > Hi Kavya,
> >
> > Most (all?) gromacs tools ignore the atom indices in the PDB file anyway,
> > so what you intend to do is straightforward.
> >
> > Kind regards,
> > Erik
> >
> > On 13 Feb 2014, at 06:30, Kavyashree M <hmkvsri at gmail.com> wrote:
> >
> > > Dear users,
> > >
> > > I was analysing the hydrogen bonding interaction of proteins and water
> > > in a simulation and was trying to extract specific water that forms
> hbond
> > > using matrix and index files generated by g_hbond.
> > >
> > > But I found that the index file created using g_hbond has continuous
> > water
> > > labels byt the pdb file of the system from the same trajectory does not
> > > have continuous labeling, eg, max atom number of water(SOL) is 99999
> and
> > > then
> > > it restarts from 0, similarly maximum residue label of water (SOL) is
> > 9999,
> > > then it restarts from 0.
> > >
> > > So if I want to use the number (of SOL) in index file generated from
> > hbond
> > > to extract respective atom in pdb file will be wrong. Kindly suggest
> me a
> > > way out
> > > of this.
> > >
> > > Thank you
> > > Regards
> > > Kavya
> > > --
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