Thank you very much sir
On Mon, Sep 9, 2013 at 5:45 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Sep 8, 2013 at 10:22 PM, Mary Varughese <maryvj1985.gmail.com
> >wrote:
>
> > sir,
> >
> > is the command below ok for dna in explicit water?
> >
> > center :1-20 mass origin
> > image origin center familiar
> > center :1-38 mass origin //Na ions
> > image origin center familiar
> > center :1-5529 mass origin// water residue
> > image origin center familiar
> >
>
> You can replace all of this with the single command:
>
> autoimage
>
> What you have now seems like overkill, especially the last one. Before
> autoimage, I would center the first molecule (or monomer, assuming you have
> multiple, disconnected subunits), image everything around that first
> monomer, then center and image again around the rest of the solute (the
> solvent will take care of itself). In the case of DNA, unless it is some
> sort of single-stranded loop, that means centering and imaging the first
> strand, then centering and imaging both strands.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 07:30:03 PDT
