AMBER: how to stop ptraj atom renumbering

From: Russell Green <>
Date: Wed, 27 Jun 2007 15:25:53 -0500

Hello all,

   I used ptraj to output pdb frames of an amber trajectory. My protein of
interest consists of several chains. The pdb output from ptraj delineates
the chains with "TER," but in doing so it also skips an atom number as such:

ATOM 12862 OXT LEU 838 93.176 55.579 118.402 0.00 0.00
TER 0 0
ATOM 12864 N ASP 839 58.015 52.149 127.257 0.00 0.00

As you can see, 12863 in this case is now missing and it causes problems
when I try to convert the pdb trajectory to a Gromacs friendly trajectory
since the number of atoms don't match up. Does anyone know how I should fix

Russell Green

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 01 2007 - 06:07:13 PDT
Custom Search