VMD-L Mailing List

From: Vasista (adupavasista_at_gmail.com)
Date: Wed Nov 01 2023 - 06:36:38 CDT

Hi, I am working on a condensate consisting of 220,000 protein atoms. For
visualization purposes, I am looking at various secondary structures formed
inside the condensate. However, STRIDE breaks by giving the following
error.

File /usr/tmp/filegkb3LC has no coordinates
Error reading PDB file /usr/tmp/filegkb3LC
ERROR) Unable to find Stride output file: /usr/tmp/fileLa9x91
ERROR) Stride::read_stride_record: unable to read output file from Stride
ERROR) Call to Stride program failed.

I have read that VMD's implementation currently supports up to 100K atoms.
I have tried a workaround by chopping the condensate by fragment into
multiple PDBs and loading them, and the STRIDE works perfectly fine. But I
am sure, I will be missing some important secondary structure elements
between the fragments, such as a beta-sheet, which will not be recognized
by STRIDE if I load the PDBs individually. Is there any workaround for this?

Thank you. 

-- 
Vasista Adupa, M.Tech
PhD-candidate, Micromechanics of Materials Group
Zernike Institute for Advanced Materials
University of Groningen
Nijenborgh 4,
9747 AG
Groningen, Netherlands
e-mail: v.adupa_at_rug.nl
office: X5113.0131 (NB4)