[gmx-users] Xe atom

[Divya Sunil]

thanks for the reply.. I am planning to place Xe in the protein binding
site ( just like a metal atom). I made a topology file with xe charge and
mass. I have two options to implement the simulation. 1. like
protein-ligand simulation. 2. replacing a number of solvent (water)
molecules with xe in the cubic system. for these purposes what is the
correct procedure?... do I need to simply add the xe parameters to .gro
file and topol file?  or may i need to make changes in forcefield?  pls help

Thanking you
Divya


On 8 July 2013 19:16, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:

> I am a too curious person not to ask WHY Xe is of interest in connection
> with the protein..?
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/8/13 9:21 AM, divyasunil wrote:
> >
> >> Hello,
> >>
> >> Please help me to add Xe atom to GROMOS96 53a6 force field. I need to
> >> carry
> >> out a protein-Xe simulation . I tried myself but failed.
> >>
> >>
> >
> >
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-- 
"A man is great by deeds, not by birth."

##################################
Dr. Divya G. Nair
Post Doctoral Fellow
Institute of Biophysics and Physical Biochemistry
University of Regensburg
Regensburg-93040
Germany
##################################