VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Tue Sep 20 2016 - 13:47:26 CDT

Hello
Just curious if there is a reason not to include some minor error checking in the vmd pdb reader for the coordinate columns.

I ran into a situation where a pdb file is generated in an upstream application, and for reasons that are being looked into, the xyz columns are all NaN in a very few files (1 out of 300K or so).

This "bug" found this while using vmd in batch mode to do some analysis and vmd was hanging at the distance check after a couple hours of running the analysis.

The vmd version is 1.9.2 so maybe this is not an issue in newer releases?

Thanks
Brian Bennion