ViewDockX for Autodock Vina error
Dear colleagues, for some reason ChimeraX does not recognize pdbqt from Autodock Vina 1.1.2 as a "docking file", even though it opens pdbqt file just fine (The message: No suitable models found for ViewDockX). The documentation says that Autodock Vina is supported. Perhaps it's the version of Vina (I use 1.1.2, or preferably its fork Smina, while the newest version is 1.2)? If I knew what the file that ChimeraX recognizes as a "model" looks like, I'd write a script to reformat my pdbqt, but at the moment I'm in the dark... Not too bad since I still can view the structures, but perhaps I'm missing some cool features... Thank you in advance, Vis
Use the Help / Report a Bug dialog and include your pdbqt file (or a smaller one the replicates the bug), and we'll be able to figure out what's going on. It could be a change in the pdbqt format, or a bug in our code. And with the example pdbqt file, we will be able to verify that any change to fix it, actually works. -- Greg On 12/12/2021 8:12 AM, Visvaldas K. via ChimeraX-users wrote:
Dear colleagues,
for some reason ChimeraX does not recognize pdbqt from Autodock Vina 1.1.2 as a "docking file", even though it opens pdbqt file just fine (The message: No suitable models found for ViewDockX). The documentation says that Autodock Vina is supported.
Perhaps it's the version of Vina (I use 1.1.2, or preferably its fork Smina, while the newest version is 1.2)?
If I knew what the file that ChimeraX recognizes as a "model" looks like, I'd write a script to reformat my pdbqt, but at the moment I'm in the dark... Not too bad since I still can view the structures, but perhaps I'm missing some cool features...
Thank you in advance,
Vis
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Are there REMARK records in the file with the string "VINA RESULT:" in them? Are those REMARK records between MODEL/ENDMDL records? --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 12, 2021, at 8:12 AM, Visvaldas K. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
for some reason ChimeraX does not recognize pdbqt from Autodock Vina 1.1.2 as a "docking file", even though it opens pdbqt file just fine (The message: No suitable models found for ViewDockX). The documentation says that Autodock Vina is supported.
Perhaps it's the version of Vina (I use 1.1.2, or preferably its fork Smina, while the newest version is 1.2)?
If I knew what the file that ChimeraX recognizes as a "model" looks like, I'd write a script to reformat my pdbqt, but at the moment I'm in the dark... Not too bad since I still can view the structures, but perhaps I'm missing some cool features...
Thank you in advance,
Vis
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Eric Pettersen -
Greg Couch -
Visvaldas K.