[gmx-users] Xe atom

[Dr. Vitaly Chaban]

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