Hi,
You may find the Amber analysis tutorial C1 on RMSD calculations with
CPPTRAJ useful:
http://ambermd.org/tutorials/analysis/tutorial1/
Hope this helps,
-Dan
On Thu, Feb 19, 2015 at 2:45 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>
wrote:
> Dear Amber List
> I did MD simulation for my ligand-protein complex in solvated form. I
> would like to do rmsd for my ligand during MD simulation and see the
> conformational changes of my ligand throughout the simulation. How can I do
> this? Is it possible to extract the trajectory of the ligand from the main
> trajectory.
> Your help in this regard would be highly appreciated.
> All the bestMaryam
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Feb 19 2015 - 08:30:03 PST
