VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 17 2002 - 10:23:08 CDT

Hi,

On Wed, Jul 17, 2002 at 07:59:11AM -0700, B. Bennion wrote:
> Hi Jeff,
>
> Is amber 7 the latest release? It seems that many folks are having
> problems with reading amber files lately.

Yes. There are also bugs in our old reader as applied to certain
Amber 6 files, so we're actually running into multiple problems
at once. The root of the problem is that our Amber 6 reader was based
on some other free Amber reader code which had various bugs.

Dave Case suggested that we take a look at Thomas Cheatham's
'ptraj' program as a reference, as it is better written than
the other examples we had looked at previously:
  http://www.chpc.utah.edu/~cheatham/ptraj.html

Here's one of the older Amber file format docs:
  http://www.amber.ucsf.edu/amber/formats.html

The current manuals should have the specs in them as well, see
them on the Amber home page:
  http://www.amber.ucsf.edu/amber/

In a way we really have two tasks to tackle:
  1) make a new Amber 7 file I/O plugin
  2) fix the bugs in the existing Amber plugin so it gets along with
     more of the Amber 6 files.

  John 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078