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Thanks! Jeff told me the forum is pretty regularly used and that I should post it here..it’s been a while since I last posted something on the mini mailing list.
Anyways, my approach seems similar to what you described in your covalently attached dye work – start with a stereospecific smile string of the modified AA, use OpenEye Omega to generate a conformer/rotamer library, use molfile_to_params.pl to generate parameters (modified to include polymer-type info), and then do some packing along with local backbone/side-chain sampling. Since we want to model diverse sets of ligands, we needed an automated method with minimal human intervention.
I grabbed the tarball in that thread. I’ll send Doug an email and see if he has anything to add. The protocol was surprisingly easy to code up and run, and seems to be generated believable structures, so props to the mini developers.