I use Rosetta 3.4 on Ubuntu 12.04 64bit.
* Question 1: Positive total_energy after relax with all-heavy-atom constraints?
I have a NMR structure model which I want to "prepare" for rosetta using relax with all-heavy-atom constraints.
Following the "short protocol" given at:
I used the 1st model of the NMR ensemble as input and generated 200 decoys. But all have positive total_energy (~120.00 REU) after relax. Does this mean the model is not very good? (I read in the same page "you should never have positive score12 scores for a well folded protein"). Or relax with all-heavy-atom constraints is a bad idea for my model?
* Question 2: is "-relax:thorough" sufficient?
So I tried to relax my model using different parameters.
Manual on "relax" suggests: "For virtually all situations it should be sufficient to use either -relax:quick or -relax:thorough and not worry about all the options."
After relax my structure using -relax:thorough, I got negative total_score values (ca. -200.00 REU) for my model. But it seems only the backbone conformation is optimized. Rotamers are not changed. Can I also relax the side chain as well?
Thanks in advance !