AMBER Archive (2008)

Subject: Re: AMBER: TERs

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 18 2008 - 10:49:55 CST

On Mon, Feb 18, 2008, Steve Seibold wrote:

> I am having a problem with the pdb "TER" commands when I make pdb files
> in amber. I have a three chain protein separated by "TER" in my original
> pdb file. However, when I use ptraj to make pdb files from my
> trajectories, the print out of the pdb file has no TER lines and hence
> does not separate the chains.

I'll leave this one up to the ptraj experts.

> If I use ptraj to make "restart" files
> then use "ambpdb" to make my pdb files, the print out does have TERs but
> in the incorrect locations. Any suggestions on what the problem is?

This is supposed to work. We will need more information in order to be able
to reproduce the problem.

...dac

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