[gmx-users] Water naming

Erik Marklund erik.marklund at chem.ox.ac.uk
Thu Feb 13 11:03:16 CET 2014

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,

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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