Re: residue numbering in dimers and trimers

From: samantha hughes <>
Date: Fri 31 Aug 2001 07:43:55 +0000

Hi Bill,

I think Christophers suggestion is an excellent one - I
personally wish this facility was already in AMBER, it would make
comparisons to PDB, and publications much much simpler.

Samantha Hughes
Department of Chemistry
Imperial College of Science, Technology and Medicine

"Bayly, Christopher" wrote:
> 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.
> Christopher
> -----Original Message-----
> From: Bill Ross []
> Sent: Thursday, August 30, 2001 1:01 PM
> To:
> Cc:
> 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
> original
> 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 Fri Aug 31 2001 - 00:43:55 PDT
Custom Search