Thanks for being willing to look at my system. I sent files and shared a
folder via dropbox, please let me know if there is anything else I can do
to help you help me solve/trouble shoot this.
Best,
Jonathan
On Mon, Jul 7, 2014 at 10:16 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It sounds like your box is relatively small compared to your system size,
> which (as you found) makes imaging very difficult. With autoimage you want
> to try and choose a molecule that is closest to all other molecules as your
> 'anchor'. By default cpptraj tries the first molecule, which is not always
> appropriate. Have you tried setting one of your other molecules as the
> anchor?
>
> Without knowing what your system looks like I can only offer general
> advice. If you could provide me (off list) with some structures or at least
> some pictures that illustrate the problems you are having I may be able to
> make better suggestions.
>
> -Dan
>
>
>
> On Sun, Jul 6, 2014 at 3:41 PM, Jonathan Gough <jonathan.d.gough.gmail.com
> >
> wrote:
>
> > Hi All,
> > Does anyone have any experience re-imaging a multi protein/peptide system
> > that is in a rectangular box?
> >
> > We are attempting to re-image thee production files of a md trajectory
> and
> > are having issues getting the system to stay within the periodic box.
> >
> > the major issue, turns out, is that because the system is rectangular it
> > shifts and "the ends" com out of the box. the system is comprised of 2
> > proteins and 2 peptides.
> >
> > the center of the system is essentially where the 15 residues of each of
> > the proteins meet.
> >
> > autoimage doesn't work as centers the first protein and a big chunk ends
> up
> > outside the box
> >
> > centering on all residues almost works, but the tails stick out and the
> > whole system ends up turning sideways, so the two edges/ends end up
> outside
> > of the box.
> >
> > centering on the 30 core (the 15 from each protein that touch at the
> center
> > of the system) ends up doing the same thing. (system ends up turning
> > sideways)
> >
> > the axis in order of shortest to longest are x, z, y.
> >
> > Is there a way to center on x/2, y/3, z/2?
> >
> > I imagine that auto image might work if one could do that. Is there a way
> > to specify coordinates to center something on?
> >
> > Any thoughts or ideas would be greatly appreciated!
> >
> > Thanks,
> > Jonathan
> > _______________________________________________
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> > 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) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 08 2014 - 07:30:03 PDT
