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

bharat gupta bharat.85.monu at gmail.com
Thu Dec 1 14:00:34 CET 2011


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
>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111201/7da3875d/attachment.html>


More information about the gromacs.org_gmx-users mailing list