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where is generate_ligens.linuxgccrelease?

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where is generate_ligens.linuxgccrelease?

Hello, everyone!

I am reading Mr. Baker's paper titled "Computational design of ligand-binding proteins with high affinity and selectivity". In the supplementary data, they used generate_ligens.linuxiccrelease to generate ligand conformers. But I can't find generate_ligens tool in my directory (~/rosetta/bin), also I didn't find any record about it in Rosetta tutorials. Anyone konws where to find it?

The version of my Rosetta is 2018.33.60351, and it's compiled by gcc. Is this tool abandoned or renamed by the new version of Rosetta?

Thanks in advance for your help!



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Thu, 2020-12-03 00:00
Nicole Deng

I'm not sure that that application was ever included in the main Rosetta distribution, let alone released to the public.

It shouldn't be necessary, though. What that application is doing is creating conformers for the match/design runs. You should be able to substitute other conformer generation programs for it, such as OpenEye Omega, RDKit, BCL, MOE, FROG, etc. Once you have the conformers in SDF/MOL2 format, you can pass them through the standard Rosetta ligand preparation process to get the params file:

Conformers generated by standard conformer generation programs should be as good or better than the ones generated by generate_ligens for most ligands. (Part of the reason the program was never added to standard Rosetta. If I recall correctly, the reason generate_ligens was even created was there were some issues at the time with the normal conformer generator being used in the Baker Lab -- issues which probably don't apply to you currently.)

Thu, 2020-12-03 07:19

OK, sir, get it. Thanks a lot for your quick reply!

Thu, 2020-12-03 22:56
Nicole Deng