From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 22 2008 - 14:01:32 CDT

Hi,
  I've found and fixed the bug that was causing this for files that
didn't have box information. If you like, I can provide you with a new
test version of VMD that includes the revised plugin, so you can try it out.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 16, 2008 at 10:43:24AM +0100, Ian wrote:
> Dear All,
>
> I have noticed a problem when writing a trajectory to the Amber "crd" format
> (using "File | Save Coordinates"). In particular, VMD does not seem to start
> a new line after writing the final coordinate of a frame. When the
> subsequent frame is appended to the file this results in a line which has
> more than the 10 coordinates proscribed by the "crd" format.
>
> To give an example, the transition between two trajectory frames looks like
> this:
>
> ...
> 40.526 35.888 44.681 41.743 32.467 43.662 41.528 33.221 56.389
> 37.440
> 36.152 55.161 37.904 35.571 55.493 39.029 34.595 56.105 40.295
> 35.276
> 56.568 41.240 34.170 55.054 41.022 36.169 54.436 36.721 34.839
> 55.118
> 35.876 34.245 54.747 52.642 52.102 54.410 51.166 52.022 53.397
> 50.936 53.171 52.117
> 51.732 52.971 53.012 49.457 53.384 54.216 48.665 53.814 53.848
> 50.742
> 50.655 53.840 49.528 50.411 53.448 51.625 49.734 53.046 51.115
> 48.443
> ...
>
> when I think it should look like this:
>
> ...
> 40.526 35.888 44.681 41.743 32.467 43.662 41.528 33.221 56.389
> 37.440
> 36.152 55.161 37.904 35.571 55.493 39.029 34.595 56.105 40.295
> 35.276
> 56.568 41.240 34.170 55.054 41.022 36.169 54.436 36.721 34.839
> 55.118
> 35.876 34.245
> 54.747 52.642 52.102 54.410 51.166 52.022 53.397 50.936 53.171
> 52.117
> 51.732 52.971 53.012 49.457 53.384 54.216 48.665 53.814 53.848
> 50.742
> 50.655 53.840 49.528 50.411 53.448 51.625 49.734 53.046 51.115
> 48.443
> ...
>
> This doesn't seem to be a problem if the file is read back into VMD, but it
> causes problems with other programs. I have not noticed the same problem
> when writing to the Amber "crdbox" format.
>
> Has anyone else noticed this?
>
> Many thanks,
>
> Ian.
>
> (I am using VMD for LINUX, version 1.8.5)

-- 
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