Re: [AMBER] renumber all residues in prmtop

From: Thomas Evangelidis <>
Date: Thu, 24 Jul 2014 10:09:06 +0300

On 24 July 2014 05:04, Jason Swails <> wrote:

> 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?
> Yes it does.

> 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.
My question was about setting the residue number of the protein to start
from a number different than 1. In that way I won't have to add 21 to every
residue during visualization, analysis (not necessarily with AmberTools)
and processing of results. I thought parmed could do that (according to an
older message of yours in the mailing list) and the most relevant section I
could find in the manual was that about RESIDUE_NUMBER. But apparently it's
not what I seek. So, eventually is there any way to change the residue
numbers of the protein in prmtop before starting the simulation?

> Hope this helps,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

AMBER mailing list
Received on Thu Jul 24 2014 - 00:30:02 PDT
Custom Search