[gmx-users] Water naming

Kavyashree M hmkvsri at gmail.com
Thu Feb 13 07:30:15 CET 2014

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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