Thanks,
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).
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
> > > > 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
> > >
> > _______________________________________________
> > 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)
> _______________________________________________
> 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
Received on Tue Jul 08 2014 - 11:30:04 PDT
