Unsolved

On my system, the following produces memory errors 3/5 of the time at the third or fourth insertion step, segmentation faults 1/5, and finishes without problems 1/5. Deleting and inserting one residue always works, but the scripts become increasingly unreliable with increasing numbers of residues deleted and inserted. If this problem is not due to a correctable mistake on my part, could someone please suggest how I might dock two domains of a protein without interference from their interdomain linker, and then restore the linker (presumably by building a loop).

Hi

I got positive results for total_score after symmetry docking. At the first time, I run the symmetry docking without native structure. the rmsd was not created in the score.fasc. I guessed maybe because I did not specify the native structure. So I use one of the reliable structure obtained from protein-protein docking as a native structure. After doing this, the rmsd is appeared in the score.fasc file. But I got the positive results for total_score. I do not know what the positive number means.

hi all,

I am trying to model a loop (using kinematic loop modeling) that is in close proximity to a ligand. So I included the ligand by converting the HETATMs into Rosetta atom types and including centroid (for remodel) and all-atom (for refine) parameter files via the -extra_res_cen and -extra_res_fa command lines. I used the script molfile_to_params.py to create the parameter files (both centroid and all-atom) and the ligand.pdb file.
[I made them from a .mol file using the .pdb file of the ligand using openbabel.... maybe there is a problem here..]

I have been trying to compute ala-scanning values using the dock design parser applications,
and I also want to specify some residues to be designed (like -resfile option in fixbb design).
Can somebody help me to define specific residues in alanine scanning?
and How to generate output file (.report file)?

Thanks for any help with this problem!