[gmx-users] Re: Looking for potential phosphate binding sites

[bharat gupta]

Hi,

Is there any way to get the averaged distributions of ions around the
protein surface.

On Thu, Dec 1, 2011 at 9:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> Yes, the phosphate ion moves around the protein but I am not able to find
>> out how many of them bind to my protein. How can that be done ??
>>
>>
> You'll have to set a definition for what you consider to be binding.  Is a
> transient contact "binding?"  Does the interaction have to persist for some
> length of time to be considered?  In any case, you can print a list of
> contacts that occur with g_dist -dist, or use more complex selection
> criteria and generate dynamic indices with g_select (see the help text for
> examples).
>
> -Justin
>
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> ==============================**==========
>
> Justin A. Lemkul
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> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
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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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