Re: [AMBER] renumber all residues in prmtop

From: Jason Swails <>
Date: Wed, 23 Jul 2014 19:04:41 -0700

On Jul 23, 2014, at 4:33 PM, Thomas Evangelidis <> wrote:

> Hi,
> Is there any way to renumber all protein residues in the prmtop (using an
> offset), or to preserve the residue numbering of the original pdb in tleap?
> I tried exporting a pdb file with ambpdb -offset 21 to renumber the protein
> residues, and then loaded the pdb file into parmed using addPDB command.
> However, the residue numbers of the protein did not change. The manual
> states that a new section named RESIDUE_NUMBER is added in the topology
> file. Its use is still unclear to me.

I'm confused. The RESIDUE_NUMBER reflected the new residue numbers generated from ambpdb, correct?

This information was primarily added to aid some analysis tools. AFAIK, cpptraj makes no use of this information (nor does sander or pmemd). So the primary use is in case you wrote your own analysis tool that required that information or if you were using a tool that made use of it.

Most tools in Amber ignore the RESIDUE_NUMBER flag and have the assumption that residues are numbered from 1 to NRES hard-coded.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jul 23 2014 - 19:30:03 PDT
Custom Search