VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 08 2005 - 13:57:01 CDT

Simon,
  What platform are you running Amber on, and how did you try to
convert them previously? It is possible that these files are so old
(you said Amber 4.1 after all) that none of the present-day packages
that work with Amber will read such old files. (current version of
Amber is 8.x) If you want to send me one of the files you're having
trouble with, I'd be happy to take a very brief glance at it.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 08, 2005 at 04:14:51PM +0100, Simon Whitehead wrote:
> Hi all,
>
> I am fairly new to the molecular dynamics/mechanics field and have some basic knowledge of Amber 4.1. I have performed a minimisation on the X-ray structure of my protein and would like to view the results but have been unable to convert the restrt (coords) and prmtop (PARM file) files from the Sander module of Amber into a pdb. I have tried to import the files into VMD (latest version running on Win XP) but to no avail. Could someone please correct me on what i`m doing wrong?
>
> Thanks
> Simon Whitehead 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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