RE: residue numbering in dimers and trimers

From: Bayly, Christopher <>
Date: Thu 30 Aug 2001 14:30:47 -0400

Hi Bill,

I would find it very useful to be able to retain the canonical PDB numbering
in a protein structure in my AMBER work. All this time, I have had to
remember what the conversions were (from AMBER to PDB and back), and due to
insertions/deletions it is not always a simple offset from the PDB numbers.
The most important few residues are easy to remember, but anything new
requires a lookup.


-----Original Message-----
From: Bill Ross []
Sent: Thursday, August 30, 2001 1:01 PM
Subject: Re: residue numbering in dimers and trimers

        The numbering scheme in the PDB file is such that it is easy to
        indentify the monomers, but I know that tleap will number all the
        residues sequentially, which can be a bit of a pain when one when
        one wants to restrain the same residues in both monomers, and later
        when translating the *.xyz or *.crd files back into *.pdb ones. I
        wonder if there is any way to persuade tleap to preserve the
        numbering scheme from the *.pdb file (or any numbering scheme which
        will allow easy identification of the monomers).
It would require some programming, adding the pdb info to the
redidue unit on input & using it for savepdb and saveamberparm.

If anyone wants to do it, I'll advise & incorporate the code
into the release.

Bill Ross
Received on Thu Aug 30 2001 - 11:30:47 PDT
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