AMBER Archive (2008)

Subject: Re: AMBER: offset residue numbering

From: David A. Case (
Date: Sat Jan 12 2008 - 01:10:08 CST

On Mon, Jan 07, 2008, Brendan Duggan wrote:

> I have a fragment of a larger molecule that I'm doing some NMR structure
> calculations on. I have been calling the first residue in my polymer,
> residue 135. Sander and leap are calling it residue 1. Can I use leap
> to introduce an offset in the residue numbering somehow? Converting
> residue numbers back and forth for the violation analysis is a nuisance
> and may introduce mistakes.

There is currently no way to do what you want, as far as I know. We have long
disucssed having some field like "pdbresnum" that would store the original
residue number and use that for some purposes (like constraints), but it is
quite tricky to get this all to work the way it should. If it were just an
offset (adding 134 to every residue number) that could be relatively easily
done. But in practice, people want to allow for inserts and deletions,
residues "numbers" like 262A, and so on.

Volunteers or suggestions are welcome. It's likely that this is one area
where sleap may help.


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