VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Wed Nov 25 2015 - 08:54:10 CST

Hello,
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.
Brian

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Gustavo Seabra [gustavo.seabra_at_gmail.com]
Sent: Wednesday, November 25, 2015 4:59 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Problem visualizing a pdbqt file generated by AutoDockTools

Dear all,

I’m 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:
https://www.dropbox.com/s/ybno7ezf60jgboq/Compound14-3U1I.pdbqt?dl=0

Thanks a lot!
Gustavo Seabra