[gmx-users] Water naming
erik.marklund at chem.ox.ac.uk
Thu Feb 13 11:03:16 CET 2014
Most (all?) gromacs tools ignore the atom indices in the PDB file anyway, so what you intend to do is straightforward.
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
> 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
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