AMBER Archive (2009)

Subject: [AMBER] change in protein ligand order

From: Hannes Wallnoefer (
Date: Tue Mar 24 2009 - 06:05:36 CDT


I have done an MD for a protein-ligand complex with amber10 and want to analyse
it with an in-house script. For that reason i need my ligand to have the
residue number 1.
By default leap generated my top-file with the protein as first entry and then
the ligand. I can change that by reading in two files for the protein and the
ligand and using the "combine" command afterwards.
But i want to keep my already produced trajectory. So my question ist, if there
is a way to postprocess the top-file, the restart files, and the trajectory
files in order to get them with a changed residue order and keep the
coordinates and the velocities at the same time?

Best regards,

AMBER mailing list