VMD-L Mailing List

From: Johannes von Langen (langen_at_imb-jena.de)
Date: Tue Jun 11 2002 - 03:17:31 CDT

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