Re: [AMBER] help in making xyz file

From: Jason Swails <>
Date: Tue, 14 Jul 2015 08:24:43 -0400

On Tue, Jul 14, 2015 at 5:14 AM, Robin Jain <>

> Dear all,
> How could i got the xyz formatted file using AMBER trajectory or Amber
> restart file.Please help me in this regard.

​There are multiple formats called "XYZ" files. In particular, there is a
version that has the very simple format:

A <X> <Y> <Z>
​B <X> <Y> <Z>

Where A and B are atom names and <X>, <Y>, and <Z> are the cartesian
coordinates​, <NATOM> is the number of atoms, and <title> is any
descriptive title (or a blank line). As far as I know, no program in Amber
reads or writes these files (since they are not used by Amber or many other
MD programs for anything). If this is the file you want to write, then
your two options are either:

1) write a PDB file using cpptraj and write a short awk/Python/perl script
to parse the PDB and write an XYZ file
2) write a PDB file using cpptraj and use OpenBabel to generate an xyz file
(Google is your friend here -- OpenBabel is pretty easy to figure out how
to use in my experience)

Alternatively, there is a Tinker-style XYZ file that is a bit more complex
as a file format (and won't work as a replacement for the XYZ file
described above). If this is the file you want, MDTraj (through the
"mdconvert" program) I *think* can do this: (In fact,
the latest version of MDTraj might be able to do the other XYZ file format
as well, you would have to check its documentation).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jul 14 2015 - 05:30:04 PDT
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