I have docked structure, different conformations from autodock, but I am not able to get how to visualize those docked structure in PyMol. Since many literature mention this but am unable to do so as am not able to save docked pose in any of the file format autodock provides i.e. PBDQT, PDBS, PDBQ, VRML, MMCIF, as they all can save single molecule.
Hi Aditi, Autodock gives output in dlg format , which is readable in MGLtools. You can download MGLtools1.5.4 or 1.5.6 and follow the instructions given in manual. In MGLtools you can visualize each conformation and interaction, also you can save them in PDB format as complex.
Dear Aditi,
you don't say the on what kinf of OS are you running Pymol, but the only way to load a dlg file obtained from Autodock is to load it via the Autodock Plugin :
http://www.pymolwiki.org/index.php/Autodock_plugin
http://wwwuser.gwdg.de/~dseelig/adplugin
that should be already installed in the latest releases.
Federico
You should be able to save the session as you have it for further work.
check this video.. it may help full for you
http://www.youtube.com/watch?v=awGrWBEk8Q0
You can use python .........................its better than pymol...............i also tried it in one of my research work...................and it gave me excellent work..........really
dear
i also agree with Vikash Kumar ·
Autodock gives output in dlg format , which is readable in MGLtools. You can download MGLtools1.5.4 or 1.5.6 and follow the instructions given in manual. In MGLtools you can visualize each conformation and interaction, also you can save them in PDB format as complex.
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