From: Bennion, Brian (
Date: Wed Nov 25 2015 - 08:54:10 CST

I have seen this issue with in my own work a long time ago. Unfortunately I dont remember the exact cause. The format of the pdbqt file in the last 3? columns may confuse/prevent determination of backbone status. The values in those columns are not standard pdb convention.

From: [] on behalf of Gustavo Seabra []
Sent: Wednesday, November 25, 2015 4:59 AM
Subject: vmd-l: Problem visualizing a pdbqt file generated by AutoDockTools

Dear all,

Iím having a weird problem trying to open a PDBQT file generated by ADT in VMD. VMD can open the file using PDB format, but only displays it as atom-based representations. Whenever I try to visualize using a backbone-based representation (ribbons, cartoon, etc.), nothing shows. Has anyone here dealt with a similar problem before?

If anyone wants to try, the file is here:

Thanks a lot!
Gustavo Seabra