AMBER Archive (2006)

Subject: AMBER: Renumber residues in LEAP

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Tue Dec 19 2006 - 15:55:57 CST

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


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