AMBER: Renumber residues in LEAP

From: Akshay Patny <>
Date: Tue, 19 Dec 2006 15:55:57 -0600

Dear Amber users

I am trying to prepare system for lipid bilayer simulation
of a GPCR. I have generated the intital system using VMD and
GROMACS and have the resulting PDB file.

I have attached the PDB file, however, deleted majority of
lipids and waters (as size was too big). In this PDB file
the coordinates for protein are first, and starts from
residue number 1-297. However, the actually the residue
number # 1 in this PDB file corresponds to residue number #
24 and so forth.

I have placed TER cards between protein and ligand and also
between each lipid and water molecules.

I am curious, is there a way in LEAP to renumber all
residues from 1- let's say 10,000 ---- To ----- like
24-10,024? How can I do that? I want my residue numbers of
protein correct as later when I look into the output from
simulation, it will create a confusion with residue numbers.

I will appreciate help.

Kind Regards
Akshay Patny

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Wed Dec 20 2006 - 06:07:53 PST
Custom Search