AMBER Archive (2003)

Subject: Re: AMBER: add

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Jul 31 2003 - 18:45:54 CDT

Hello,

This seemingly simple task is apparently uncommon.
There are several paths that one may pursue.

1. model_plus_trp = sequence {model TRP}
  this will bond TRP onto the tail of model if model's
  last residue has the appropriate connect atom.

2. model_with_trp = combine {model TRP}
  similar to above, but without bonding.

3. use the GUI to build the TRP onto model.

4. myTRP = copy TRP; add model myTRP
  in fact, this does not work since myTRP seems to carry
  the same containment information as TRP.

Good luck,
Scott Brozell

On Thu, 31 Jul 2003, Ran Ye wrote:

> 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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