Hi Members
I am looking at the interaction of ethanol with a particular protein. After
developing the model I docked the ethanol using the autodock-Vina and found
some binding sites. I ran 10 ns MD for the best binding sites provided, but
when visualizing the trajectories form vmd I found that some are not stable
and ethanol going outside the binding site ( outside the protein as well).
However when checking rmsd of the ethanol molecule using ptraj giving the
reference to the first frame I do not see larger rmsd variations. Can
anyone please explain what is the reason for that and how I can see the
stability of ethanols without visualizing in vmd.
Thank You
--
Chinthaka Nadun Ratnaweera
Hand Lab Rm 1126
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Tue Feb 05 2013 - 09:00:02 PST
