On Tue, Jul 8, 2014 at 12:17 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> I thought that to get teh RMSD data and to run MMPBSA the entire system had
> to stay within a single box (or else you got some really weird things going
> on).
>
You just need to make sure you don't have any imaging artifacts, e.g. the
second unit of your dimer gets imaged while the second unit does not,
resulting in an artificial-looking split. This can be easily detected by
large jumps in the RMSD of the dimer w.r.t. the first frame, etc. As long
as there are no imaging artifacts you should be ok.
-Dan
> Is that not the case? We also wanted to do PCA and believed we needed the
> same thing as well.
>
> Can you take an existent solvent box and add water to it (make it bigger)?
> Or do we need to start all over with the naked protein again?
>
>
> On Tue, Jul 8, 2014 at 1:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > I received your files, thanks. I ran autoimage on your trajectory and it
> > worked, insofar as your molecules do not separate (i.e. there are no
> > imaging artifacts). The issue here is that I think your box is way too
> > small to prevent your system from "feeling" its images. Note that the
> > system is never really outside the box since you have periodic boundary
> > conditions. What is happening is that your system is rotating to
> > accommodate it's neighboring images. Unless you really need the box to be
> > small because you're trying to study the system at a particular
> > concentration, you should increase your box size, and maybe even change
> to
> > a truncated octahedron.
> >
> > Hope this helps,
> >
> > -Dan
> >
> >
> > On Tue, Jul 8, 2014 at 8:12 AM, Jonathan Gough <
> jonathan.d.gough.gmail.com
> > >
> > wrote:
> >
> > > 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
> > > > > _______________________________________________
> > > > > AMBER mailing list
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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) 585-6208 (Fax)
> > > > _______________________________________________
> > > > AMBER mailing list
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> > > >
> > > _______________________________________________
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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) 585-6208 (Fax)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> 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) 585-6208 (Fax)
_______________________________________________
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Received on Tue Jul 08 2014 - 12:30:02 PDT
