Re: AMBER: connecting a non standard residue to the rest of an enzyme

From: David A. Case <case.scripps.edu>
Date: Fri, 23 Nov 2007 10:39:13 -0800

On Fri, Nov 23, 2007, Bouthe´na Kerkeni wrote:
>
>
> I have created a non standard residue that is a part of an enzyme.
> Now I have the file.lib, file.pdb, and the original pdb is original.pdb
> The problem being that the Fe-SG-CB I cut out in file.pdb belong to
> the same residue of the rest of cysteines CA-N-C-O. I have changed
> the named of the all CYS connected to the non stadard part to CYX,
> but xleap complains about name change in pdb file. Also
> In xleap,
> >loadoff file.lib
> >original=loadpdb original.pdb
> >edit original
> This gives me twice the atoms in the file.pdb translated w respect to
> each other + the cysteine atoms + new SG and CB atoms and H atoms.

You are almost certainly going to need to provide more details: what exactly
did you do, what was the "complaint" that xleap gave? etc.

I think it will be almost impossible to load the original pdb file -- you will
have to edit it so that the atom names match those of your non-standard
residue, and there is an exact one-to-one relation between the library files
and the pdb you load.


...dac

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Received on Sun Nov 25 2007 - 06:07:40 PST
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