AMBER Archive (2003)

Subject: Re: AMBER: add

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Jul 31 2003 - 16:51:46 CDT

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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