[gmx-users] HYDROGEN BOND EXISTENCE MAP

[Neha Gupta]

Thanks.

On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevan <isheeja at iitb.ac.in>
wrote:

>
> Hi Neha,
>
> If I understand correctly pdb file is used for extracting information
> about the topology of the molecule..in this case the atom name and type.
> so it does not matter at which time point of time in your simulation your
> pdb file is generated as long as it is whole molecule.
>
> Best
> Sheeja.
>
> > Hi gromacs users,
> >
> > In the perl script to calculate hydrogen bond %, the command is
> >
> > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
> >
> >
> > What should the structure.pdb file contain?
> >
> > How to obtain it?
> >
> > At which point of simulations?
> >
> > Thanks,
> > Neha
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