should rosetta3.1 do prepacking before docking?

[Anonymous]

I switched from rosetta2.3 to rosetta3.1 recently and I found that flags are changed in the new edition. I used to do prepacking before docking in rosetta2.3, should I do the same thing in rosetta3.1? Also, I used to do both perturbative docking and ensemble docking using rosetta2.3, could I do the same kind of thing using rosetta3.0?

Anyone knows the answers? Please share with me and I really appreciate that. Thanks a lot.

[Anonymous]

The prepacking flag is docking:dock_ppk. It’s not clear to me, but it may be that you have to run prepacking as a separate job before your regular run.

[Anonymous]

I know that in rosetta2.3, I have to do prepacking before regular run. Is the prepacking step still necessary in rosetta3.1? Could I just do full atom docking without that step? Thanks a lot.

> I switched from rosetta2.3 to rosetta3.1 recently and I found that flags are changed in the new edition. I used to do prepacking before docking in rosetta2.3, should I do the same thing in rosetta3.1? Also, I used to do both perturbative docking and ensemble docking using rosetta2.3, could I do the same kind of thing using rosetta3.0?
>
> Anyone knows the answers? Please share with me and I really appreciate that. Thanks a lot.

[Anonymous]

It’s not a question of whether or not you “have to” for the sake of the program – it’s a question of the quality of the results. Rosetta3 will allow you to not prepack but it’s probably a good idea. Try it without and see if you like the results; if not try again with it.

[Author]

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