Re: [AMBER] Renumbering

From: Gustaf Olsson <>
Date: Thu, 17 Dec 2020 10:45:01 +0000

Realising that some additional information would make it a lot easier to answer.

I am constructing a short peptide using LEaP and saving it as a PDB file.

Constructing a simulation system I have the option to renumber residues sequentially in the produced system PDB file. I can leave the peptide in the system PDB numbered from 1-4 and then the next molecule starting at 5 and onwards. Or I could renumber the entire peptide as residue 1 and then continue with 2 and so forth.

This could make life somewhat easier when preparing input for analyses later on, especially if there are numerous peptides in the same simulation. I got a bit concerned though thinking about what would happen if trying to use (for example) “bond” in leap, it would involve setting the bond between 1 and 1.

Rather than trying to exhaust any concern I can think up I though I would ask and see of someone else had already done this and could provide some suggestion if I should maintain residue numbering in peptides from leap or renumber.

Best regards
// Gustaf

> On 17 Dec 2020, at 11:29, Gustaf Olsson <> wrote:
> Would there be any obvious problem with renumbering AAs in a peptide to a single residue number?
> LEaP output for a 4 AA peptide gives residues 1-4 as one molecule. Changing this to residue 1 for all AAs, can this cause any unintended/unexpected issues?
> Best regards
> // Gustaf
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Received on Thu Dec 17 2020 - 03:00:02 PST
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