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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
366 stars 101 forks source link

Standard output #218

Closed pnakliang closed 1 year ago

pnakliang commented 1 year ago

I have a general question regarding the output files. can I convert the dlg file to an AutoDock vina output file format?

diogomart commented 1 year ago

What is the end goal? The SDF format is better for software interoperability, see mk_export.py from Meeko.

pnakliang commented 1 year ago

What is the end goal? The SDF format is better for software interoperability, see mk_export.py from Meeko.

I have tried that, but it doesn't work well because I did prepare the ligand using mk_ligand_prepare.py from Meeko

diogomart commented 1 year ago

The DLG is a PDBQT with extra info, the following may be good enough, depending on what the use is:

grep ^DOCKED results.dlg | cut -c 9- > docked.pdbqt
pnakliang commented 1 year ago

Thank you, it's very helpful

tubiana commented 1 year ago

I just post the command with openbabel as well just in case some people want it...

obabel -ipdbqt results.dlg -opdbqt -O docked.pdbqt -ad

NOTE: the -ad precise the d argument for the pdbqt READING format. (check https://openbabel.org/docs/current/FileFormats/AutoDock_PDQBT_format.html#read-options and https://openbabel.org/docs/current/FileFormats/Overview.html for how to give input/output arguments).