From: Himanshu Khandelia (
Date: Thu Jan 18 2007 - 09:55:07 CST


Often, after deletion of overlapping water molecules, the psf and the pdb
contain non-sequential residue numbers (like 2,4,5,6,10) instead of
(1,2,3,4,5). Although this does not present a problem in NAMD analysis and
simulation, it might pose difficulty if the trajectories produced by NAMD
are exported to and analyzed in CHARMM. Even otherwise, it makes better
sense to have sequential residue numbers.

Does anyone have an available script that will renumber a multi-segment
pdb and the psf sequentially, or even parts of the pdb and psf
sequentially ?

Thank you for the help,