[gmx-users] script to add water in protein

[Tsjerk Wassenaar]

Hi Pooja,

Do you mean solvating around the protein, or placing water inside? If you
feel brave, you can check out the C code of genbox. Genbox copies a box of
solvent to cover the box with the protein, and then removes all solvent
which has overlaps with the protein.

Cheers,

Tsjerk


On Mon, Aug 12, 2013 at 9:43 AM, <pooja_gupta at nccs.res.in> wrote:

> Thanks
>
> I am looking for code (python, C++), not gromacs command line.
>
> pooja
>
>
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
> >
> >
> > On Mon, Aug 12, 2013 at 4:09 PM, <pooja_gupta at nccs.res.in> wrote:
> >
> >> Hi
> >>
> >> I want to add water molecule in my structure. Do anyone have idea how to
> >> add water molecules in protein structure. I little aware of python.
> >> How the gromacs spc216 add the water molecule. Can i get the code for
> >> the
> >> same?
> >>
> >> pooja
> >>
> >> --
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-- 
Tsjerk A. Wassenaar, Ph.D.