Ms. Aswathy S wrote:
Hi,
After minimizing the protein -ligand complex, the co-ordinates have changed
drastically.My idea about minimization was the coordinates will have minute
changes only. In this case my protein is completely transferring to a new
co-ordinates.Is that reasonable.??
The amount of change will depend on the quality of the initial model. If large
changes need to be made, they can be. If the entire protein is moving, then
perhaps the box has not been prepared correctly, and the translation is caused
by a periodic jump. Have a look at the output (not just the coordinates) and
see if you can deduce what's going on.
-Justin
Thanks, Aswathy Dept. Biotechnology Ext. 3108
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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