Hi,
Without knowing what ptraj/cpptraj input you have tried it's difficult
to give detailed advice, but I think what you want to do is take the
no-fit RMSD of the ligand after fitting on the initial receptor
(assuming it has ligand bound), e.g.:
rms first :1-N
rms first nofit :LIG out ligand.rmsd.dat
Where N is the number of residues in your receptor and LIG is your
ligand residue name.
-Dan
On Tue, Feb 5, 2013 at 9:37 AM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Feb 05 2013 - 10:30:03 PST
