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