Re: Bin Coordinate file to pdb

From: Chris Harrison (
Date: Thu Jul 08 2010 - 18:26:51 CDT

Dear Philip,

Use VMD.

Open TKconsole under Plugins menu and type in TKconsole:
mol new mypsffile.psf
mol addfile mybincoords.coor
set sel [atomselect top all]
$sel writepdb mynewpdb.pdb

You should probably work through the tutorials for a basic understanding of
how you can use VMD and NAMD for your work, in general:

*Using VMD* (html <vmd/tutorial-html/index.html>) (pdf<vmd/vmd-tutorial.pdf>,
1.6M) (required tutorial files <vmd/vmd-tutorial-files.tar.gz> [.tar.gz,
44.9M], [.zip <vmd/>, 44.9M], individual
Participants build an image of ubiquitin while becoming familiar with basic
VMD commands. Additionally, participants learn how to look for interesting
structural properties of proteins using VMD. Tutorial works on Windows, Mac,
and Unix/Linux platforms. The previous version of the tutorial can be found
here <vmd-old/>.

*NAMD Tutorial*
(html for Unix/Mac <namd/namd-tutorial-unix-html/index.html>) (pdf for
Unix/Mac <namd/namd-tutorial-unix.pdf>, 7.9M)
(html for Windows <namd/namd-tutorial-win-html/index.html>) (pdf for
(required tutorial files (all platforms)
<namd/namd-tutorial-files.tar.gz> [.tar.gz,
148M], [.zip <namd/>, 148M], individual files (all
platforms) <namd/namd-tutorial-files/>)
Participants learn how to use NAMD to set up basic molecular dynamics
simulations, and to understand typical NAMD input and output files, with an
emphasis on such files for protein energy minimization and equilibration in
water. Tutorial versions available for Windows, or Mac and Unix/Linux


On Thu, Jul 8, 2010 at 3:50 PM, Philip Peartree <> wrote:

> Hi All,
> Is there any way of converting a binary coordinate file as generated by a
> namd simulation into a pdb file?

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078

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