[gmx-users] Water naming

[Kavyashree M]

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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