From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Nov 25 2015 - 10:41:57 CST

Hi Brian,

Thanks a lot! Apparently, VMD isnít able to open PDBQT files then. I wonder if there are plans to add this functionality to VMD any time in the foreseeable future.

All the best!
Gustavo Seabra

> Em 25 de nov de 2015, ŗ(s) 11:54, Bennion, Brian <Bennion1_at_llnl.gov> escreveu:
>
> 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,
>
> 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:
> https://www.dropbox.com/s/ybno7ezf60jgboq/Compound14-3U1I.pdbqt?dl=0
>
> Thanks a lot!
> Gustavo Seabra
>
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>
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