AMBER Archive (2003)

Subject: Re: AMBER: add

From: Ran Ye (ryejob_at_yahoo.com)
Date: Thu Jul 31 2003 - 17:03:43 CDT

I have read the manual P.41 word by word but still
confused about how can I add a residue (say, TRP) to
an existing UNIT (loaded from a PDB file)? Thanks a
lot!

--- Scott Brozell <sbrozell_at_scripps.edu> wrote:
> Hello,
>
> As the manual indicates
> add a b
> will only work if the object b is not contained by
> another object.
> The residue TRP.1 (see the ouput of desc TRP.1) is
> contained
> in the unit TRP (see the ouput of desc TRP).
> Hence r, which refers to TRP.1, is already contained
> in unit TRP.
> Admittedly the error message could indicate the
> containing object.
>
> See the example usage of add in combination with
> create commands
> on page 41 of the manual.
>
> Scott Brozell
>
> On Thu, 31 Jul 2003, Ran Ye wrote:
>
> > Hi Amber Users,
> >
> > I have a quick question which I couldn't figure
> out:
> > when I try to use "add" command in xleap, it
> always
> > complains "The object r is already contained
> within".
> > Does anyone have an idea? (for example,
> model=loadpdb
> > "aaa.pdb", r=TRP.1, add model r, is there any
> obvious
> > problem I missed?)
> >
> > Thanks a lot!
> >
> > Ran
> >
>
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