VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 12 2002 - 01:18:34 CDT

Dear Johannes,
  All of the file reading/writing code in the new pre-release version
of VMD has been seriously re-worked, and so it is likely there are
new bugs/problems that need to be fixed, so its VERY useful to know when
people have trouble with this pre-release version, as we will take a look
at the new code and see what's causing these problems. Can you try loading
the same files in VMD 1.7.1 and VMD 1.8a10 and tell us how their behavior
differs? Alternately, if you have files you can let us have copies of,
we'd love to be able to use these to test locally. The Amber file readers
are currently in the process of being re-vamped, as there were several
limitations in the old VMD code preventing certain kinds of Amber 6 files
from being loaded correctly, and we are writing new code in order to read
the Amber 7 files now. If you're willing to let us get copies of the
files that cause problems on VMD 1.8, that will make testing these
file readers easier for us. I'll see what we can do about this before
the next alpha version is made available. We've already fixed quite a
large number of other bugs/problems that users reported from the alpha 10
version, so the next alpha version should go more smoothly in most cases.

  John

On Tue, Jun 11, 2002 at 10:17:31AM +0200, Johannes von Langen wrote:
> Dear VMD users,
>
> excited about the new release of vmd 1.8(a10) I tried to load one of my
> AMBER (6.0) trajectory files. Unfortunately with no success:
>
> As the parameter file I loaded the amber *.top file (like I allways do
> in vmd-1.7) and for the coordinates I loaded the *.crd trajetory, which
> in most cases worked in earlier vmd releases (besides some "Exceeded
> maximum number of bonds" sometimes). On vmd-1.8 the first frame is
> loaded normally, but on the following ones vmd puts up strange bonds
> between the water-molecules (with bondlengts exceeding 10 to 70
> Angstroem) and the same in the protein. Any one else experienced this
> strange "new" behavior?
> Maybe it's because of the periodic conditions and the box-information in
> the *.top and *.crd files, but vmd-1.7 had no problems with that.
> Earlier in this mailing-list are comment about strange bond lengths
> (although they seem to relay on the automatic bond search in vmd, what
> looks diffenent to my problem) that can be solved by using psfgen. As I
> only have amber-files I can't find a way of using psfgen - any
> suggestions/experiences?
> Why is the first frame and parts of some of the following frames loaded
> correct, but 99% of the frames are strange?
> Thanks for any help.
>
> John
>
> p.s.:
> there are no double waters like mentioned in an earlier discussion - but
> approx. 9800 watermolecules
> and:
> when I let amber (ambpdb) write out a pdb-file, vmd can load it with no
> problems - this also applies to the files, that have parts of it with
> the message "Exceeded maximum number of bonds" loaded (there normally
> one residue has got very strange bonds...)
> --
> Johannes von Langen langen_at_imb-jena.de
> Institut fuer Molekulare Biotechnologie
> Beutenbergstrasse 11, Jena Tel.: +49-3641-65-6213
> Postfach 100 813, D-07708 Jena, Germany Fax: +49-3641-65-6210 

-- 
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