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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
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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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