Justin A. Lemkul wrote:
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.
Try running g_confrms to see whether they really are very different.
-Justin
Thanks, Aswathy Dept. Biotechnology Ext. 3108
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________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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