Re: [AMBER] CHAMBER and making PDB files

From: Ross Walker <>
Date: Wed, 1 Jun 2011 10:49:55 -0700

Hi Steve,

The position of the coordinate origin in files built with Charmm and then
processed through Chamber is different to that for Amber files built through
Leap. This does not cause any simulation issues but it does present an
imaging issue that means visualizing files can be a little confusing.

The solution is to image things first in ptraj before writing the pdb file.
You probably want to do this before visualizing trajectories as well.

Try adding, where XXX is the last residue number in your solute.

center :1-XXX mass origin
image origin center familiar

You might need to tweak this a little bit to get it to work but that should
get you started.

All the best

> -----Original Message-----
> From: Seibold, Stephen []
> Sent: Wednesday, June 01, 2011 10:35 AM
> To:
> Subject: [AMBER] CHAMBER and making PDB files
> Hello
> I used CHAMBER to create a AMBER topology file and input coordinates. I
> then obtained, doing MD, a restart file which I am trying to make a pdb
> file from. I saw, online, that "ambpdb" would not work but that ptraj
> would. I tried this and it did write out a pdb file but the last 10-11
> residues on terminus were placed away from the protein.
> Any ideas on how to fix this? Is it something I am doing?
> I am sending you the pdb file and the output which does say there were
> errors, but not what they were...Just "in reading the prmtop file".
> Steve

AMBER mailing list
Received on Wed Jun 01 2011 - 11:00:07 PDT
Custom Search