Thanks. This is what I wanted to ask.
Regards,
Mish
On Wed, Jun 4, 2014 at 6:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I think I may have not understood you again, sorry. I think you're
> asking if you can use two molecules as an anchor, right? If so that
> cannot work; the way that autoimage works it can only use 1 molecule
> as the anchor. That anchor should be the molecule that on average is
> close to everything you want together in your system. By default
> cpptraj chooses the first molecule, but as you've probably seen that's
> not always the best choice. Most times which molecule the anchor
> should be is clear, but you may need to experiment a bit to find out
> which one looks the best to you.
>
> Anyway, hope this clears things up - sorry for the confusion.
>
> -Dan
>
> On Wed, Jun 4, 2014 at 11:15 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > On Wed, Jun 4, 2014 at 9:43 AM, mish <smncbr.gmail.com> wrote:
> >> Yes, they are two molecules in terms of they they are written in
> topology.
> >> Residues 2-114 and 115-229 are two domains of a protein. I was not clear
> >> enough in my previous email, probably.
> >
> > Actually, I think I wasn't clear enough. The reason I asked you to run
> > the command 'molinfo !:WAT' (actually, even better would be 'molinfo
> > :2-229') was to see how cpptraj thinks the molecule layout should be
> > so I can start debugging. If CPPTRAJ thinks they are one molecule that
> > may be an issue with how cpptraj is reading the topology, but if it
> > thinks there are two molecules that is an issue with 'autoimage'
> > itself. If you could provide me off-list with a topology and restart
> > file so I can try and reproduce the problem that would be ideal.
> >
> > Also, what version of cpptraj are you using? If not V14 (from
> > AmberTools 14) you should definitely upgrade.
> >
> > -Dan
> >
> >>
> >> I want to know if it is possible to assign multimeric structure as
> anchor
> >> residues or not (or can be only one as it is returned in the error) ?
> >>
> >> only autoimage followed by center the whole complex in the periodic cell
> >> (image origin center) works fine.
> >>
> >> Thanks
> >> Mish
> >>
> >>
> >>
> >> On Wed, Jun 4, 2014 at 4:26 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >>
> >>> Hi,
> >>>
> >>> Are you sure residues 2-229 do not span two molecules in your
> >>> topology? What is the output of 'molinfo !:WAT'?
> >>>
> >>> -Dan
> >>>
> >>> On Wed, Jun 4, 2014 at 9:11 AM, mish <smncbr.gmail.com> wrote:
> >>> > I have a question related to autoimage task in cpptraj. I would like
> to
> >>> > center complex (a ligand followed by a diamer protein in top file)
> during
> >>> > imaging but assigning anchor to protein seems not work.
> >>> > input file:
> >>> > parm solvated.parm7
> >>> > trajin traj1.dcd
> >>> > autoimage anchor :2-229
> >>> > trajout traj-imaged.nc netcdf
> >>> >
> >>> > .....................................................
> >>> > ACTION SETUP FOR PARM 'solvated.parm7' (1 actions):
> >>> > 0: [autoimage anchor :2-229]
> >>> > Mask [:2-229] corresponds to 2 molecules
> >>> > Error: Anchor mask [:2-229] corresponds to 2 mols, should only be 1.
> >>> > ------------------------------------------------------------
> >>> >
> >>> > I think its taking both monomers as a molecules and generating
> error. I
> >>> am
> >>> > sure there will be some way to do it, but would I like to know if it
> can
> >>> be
> >>> > done using autoimage.
> >>> >
> >>> > Thanks
> >>> > Mish
> >>> > _______________________________________________
> >>> > 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
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
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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)
>
>
>
> --
> -------------------------
> 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 Thu Jun 05 2014 - 08:00:10 PDT
