VMD-L Mailing List

From: Elizabeth Wait (elizabethewait_at_gmail.com)
Date: Thu Jun 06 2019 - 15:46:40 CDT

Hello, VMD users.

I am somewhat new to VMD (3 weeks). I have a trajectory of 5013 frames
which I am viewing on an Ubuntu computer.
When I load the trajectory (xtc) into the molecule, which I load with a
pdb, I can play the trajectory and everything works fine.
If I save the visualization state and open it again later, secondary
structure is not recognized. In New Cartoon, the protein looks like gray
spaghetti. All of my representations load fine, but even sequence viewer
does not show any secondary structure.

This is the error I receive:

ERROR) Unable to find Stride output file: /tmp/fileYel4Lr
ERROR) Stride::read_stride_record: unable to read output file from Stride
ERROR) Call to Stride program failed.

I have made sure that Stride exists and the right path is in my bashrc.

I can open visualization states with my pdb, or pdbs and smaller
trajectories (such as the files from the tutorial) and secondary structure
is recognized properly.

I have told vmd to write stride SS files to ~/.vmdtmp/ rather than /tmp
which should help if the issue is having sufficient memory.

Unfortunately, none of this helped. I have reduced my trajectory and pdb to
only protein, GTP, and Mg and that works fine, but in some cases I may need
to consider interactions with solvent and membrane. Would anyone be so kind
as to offer any suggestions of what I can do?

Thank you,
Elizabeth