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

[Justin A. Lemkul]

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

========================================