AMBER Archive (2005)

Subject: Re: AMBER: pdb files from traj file

From: David LeBard (david.lebard_at_asu.edu)
Date: Wed Jul 13 2005 - 16:30:07 CDT

Hi Young-Jin,

If you read your trajectory and topology files into VMD, you can output
every configuration (or configurations at certain intervals) using VMD.
You can do this easily by 1) Load the topology file (parm7) as a new
molecule, then 2) Add your mdcrd data file (either crd for non-periodic
simulations or crdbox for periodic) to the newly molecule, and 3) After
the data is loaded, from the VMD Main window go to File -> Save
Coordinates. This makes pdb (and other) files based on your trajectory
data. The files names have a number appended to them to account for
their position in the trajectory. This is a 0-based array, so a 2000
step trajectory file will have pdb names from molecule.pdb.0 to
molecule.pdb.1999.

Hope this helps.

Best,

David LeBard
Dept of Chemistry and Biochemistry
Arizona State University

On Wed, 2005-07-13 at 14:06, YoungJin Cho wrote:
> Let me ask very simple question.
>
> Does anybody know how can get a pdb file from traj file?
> Not only the final pdb but also the others: I can see those from vmd
> but I have no idea how I can save them as pdb file. (So my question is
> how we can get pdb files from one traj file)
>
> Thanks in advance,
>
> Young-Jin
>
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