Thank you Dan
This works fine for me. Initially what I did was try to find the rms of
ligand with the following command.
rms first out test.dat :N
N is the residue number of the ligand.
I am curious to know what this 'nofit' flag does here.
On Tue, Feb 5, 2013 at 12:13 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 11:00:03 PST
