First of all, thanks for sharing this code. I am having a little bit of confusion with the minimize functionality. I am relatively new to docking/minimization/scoring, and there doesn't seem to be that much documentation about what exactly is going on. I have gotten it to work by looking at other folks' code, but it seems like the output to --minimize is a ligand pdb. Does it not minimize the protein as well? Is there a way to make it minimize the protein and ligand jointly?
Thanks!
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If you enable flexible residues in the protein the side chains will be optimized as well, but smina is for high throughput molecular docking - if you want a full minimization of the system (including the backbone) you'd be better off with a molecular dynamics package or rosetta.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
First of all, thanks for sharing this code. I am having a little bit of confusion with the minimize functionality. I am relatively new to docking/minimization/scoring, and there doesn't seem to be that much documentation about what exactly is going on. I have gotten it to work by looking at other folks' code, but it seems like the output to --minimize is a ligand pdb. Does it not minimize the protein as well? Is there a way to make it minimize the protein and ligand jointly?
Thanks!
If you enable flexible residues in the protein the side chains will be optimized as well, but smina is for high throughput molecular docking - if you want a full minimization of the system (including the backbone) you'd be better off with a molecular dynamics package or rosetta.
Thanks for the help! Flexible side chains are good enough for me.