[gmx-users] Xe atom

[Dr. Vitaly Chaban]

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
> ##################################
>