VMD-L Mailing List

From: Ian (ian2craig_at_gmail.com)
Date: Wed Jul 16 2008 - 04:43:24 CDT

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)