[gmx-users] Xe atom

[Divya Sunil]

ok thank you very much. i will try and get back to u

regards
divya


On 11 July 2013 14:26, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:

> Indeed.
>
>
> So, go to your main topology file and define a new atom type "Xe" under an
> appropriate section. Then just add sigma and epsilon in the non-bonded
> section and you are ready to explore the binding.
>
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil <divyasunilkumar at gmail.com
> >wrote:
>
> > ya.. but there is experimental data to confirm the presence. can you help
> > me to solve this problem
> >
> >
> > On 9 July 2013 11:54, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
> >
> >> Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will
> >> obviously not sit in the binding site....
> >>
> >>
> >> Dr. Vitaly V. Chaban
> >>
> >>
> >> On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil <divyasunilkumar at gmail.com
> >> >wrote:
> >>
> >> > 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
> >> > ##################################
> >> >
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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
> > ##################################
> >
> --
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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
##################################