[gmx-users] Umbrella sampling of phosphate ion binding

[bharat gupta]

does the gromacs force field has topology and ff parameter for H2PO4(-) ion
. As I have derived both topology and FF parameter from prodrug server and
after checking the topology I found that it has deleted of the hydrogen.

On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> Hi Justin,
>>
>> I am having following doubts regarding umbrella sampling of phosphate ion
>> binding to my protein .
>>
>> 1. As per the tutorial, I need to fix an immobile reference. In my case
>> which region do I have to fix as my protein consists of one single chain.
>> Since  I am studying the binding and unbinding of ion, shall I fix the ion
>> fixed. If it's so, then do I have to give a different chain name for it as
>> my complex doesnot chain name for ion/ligand.
>>
>>
> You don't need an immobile reference just because my tutorial did.  I had a
> particular need to do so.  For your purpose, I highly doubt it's necessary.
> You're looking at small molecule-protein interactions, not protein-protein
> interactions.
>
>
>  2. What should be the size of box and how do I know where to place the
>> protein's COM in box (the precise location).
>>
>>
> The absolute COM is somewhat irrelevant; all distances during pulling are
> relative.  You can place the protein in a certain location in the box for
> convenience if you like.  The box size must be greater than twice the pull
> distance, as explained in the tutorial.  The amount that you wish to pull
> will dictate both the location of the protein and the box size.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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