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.
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
> > _______________________________________________
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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)
>
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>
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Received on Wed Jun 04 2014 - 09:00:03 PDT
