VMD-L Mailing List

From: Adam Gross (asgross37_at_gmail.com)
Date: Tue Mar 08 2022 - 11:39:05 CST

Hi,

Running into a challenge when trying to automate saving DCD files from VMD
for further analysis with custom-built python codes. When I save the DCDs
via the GUI, everything works fine, and I can read the DCDs no issue.
However, when I try to save using "animate write ...' I run into problems
(animate write dcd filename.dcd waitfor all). When loading the DCD with my
python code, I get an error when trying to read the "title" section of the
Header (the second block of data in the DCD, as shown here
https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html). It
occurs on the second entry of the title section. The first says 'Created by
DCD plugin', but when trying to read the second, Python gives me an error
of 'utf-8 codec can't decode byte 0xe9 in position 76: invalid continuation
byte'. When reading what should be the same DCD, except saved from VMD via
the GUI instead, that title entry contains the date ('REMARKS Created XX
Month, Year at HH:MM')

VMD itself is able to read/load both saved DCD types correctly and without
error. Running v1.9.2.

Any ideas to fix? Why is the DCD title block being saved differently when
saved via GUI vs the animate write command? And/or what type of encoding is
being used in the second line of the title section of the DCD header when
it is saved via the 'animate write' command?

Thanks