VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Mon Jul 03 2023 - 04:19:11 CDT

Hello,

I have merged several simulation files in order to run PCA and compare wildtype and mutants. I used catdcd to write backbone only files of all the simulations and then used catdcd again to combine the various backbone simulations. However, when I am trying to run analysis with Bio3D, I get the following error:

Warning messages:
1: In readChar(trj, 80) : truncating string with embedded nuls
2: In readChar(trj, 80) : truncating string with embedded nuls
3: In dcd.header(trj, verbose) :
  Check DCD header data is correct, particulary natom

I also noticed in a plot of PC1 vs. PC2 that it appears there are missing chunks of residues throughout the protein.

However, when I load the merged dcd file into VMD, I see there are 1678 atoms as I expected based on the backbone index file I created. Therefore, it seems that the header of the DCD file is causing issues in Bio3D. Is there a way to fix the header of the DCD file to reflect the correct number of atoms?

Best,
Christos