Re: [AMBER] renumber all residues in prmtop

From: David A Case <>
Date: Thu, 24 Jul 2014 08:02:33 -0400

On Thu, Jul 24, 2014, Thomas Evangelidis wrote:
> 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.

Here is the expected usage pattern: you use "add_pdb" to add information from
the original pdb file into the prmtop file. As Jason says, right now, Amber
most ignores these sections. The exception is when you use ambpdb or cpptraj
to create new pdb files (say from the frames of your trajectories). If you
add the "-ext" flag, the residue numbers (and other information like chainIDs
and alternate location flags) from the original PDB file are put into the
output PDB file.

If you then carry out analysis or visualization using these PDB files, the
original residue numbering (etc.) will be present.

This is, for sure, only a partial solution. This original PDB info is not
used in most circumstances in AmberTools. In our defense, it can be very hard
to do analyses when residue numbers are not continuguous, monontonic, or even
numbers at all (as when there are insertion codes [letters] in PDB entries.)

....hope this helps....dac

AMBER mailing list
Received on Thu Jul 24 2014 - 05:30:02 PDT
Custom Search