Unsolved

I am having troubles with terminal caps in FlexPepDocking in Rosetta 3.5. In the input PDB files the receptor and peptide contain ACE and NME at the N- and C-terminus, respectively. Rosetta does not recognize the modified terminal residues as N_acetylated and C_methylamidated. I have carefully modified the ACE/NME atom names to correspond to the Rosetta naming scheme in the corresponding residue patch files.

I'm new to Rosetta and learning demos.

I tried rosetta-3.5/rosetta_demos/public/calculate_e6ap_ubch7_ddgbind
to calculate ddG by mutation, but the average difference between dg_wt
and dg_mut converges to zero, of all 5 mutations in the demo.

I used the command below to calculate scores, using a relaxed structure
calculated before. The mutation_script.xml is attached, same as provided
in the demo except removing <Add mover_name=relax/>.


rosetta_scripts.linuxgccrelease
-database $ROSETTA3_DB
-s relaxed_1C4Z_0001.pdb
-ignore_unrecognized_res

I am trying to use loop_modelling. I have small problem on my loop modeling problem. I have missing residues in protein. I gave these missing residues as blank in input pdb. My loop_modelling execution was successful however I did not solve my problem. I am wondering - can Rosetta add missing residues using loop modeling protocol? If so, how can be list of missing residues given in the program (parameter)? If not, could you please tell me any suggestion to put missing residues in the protein during loop modelling?

Hi,

I used Calibur to cluster my structures produced by Rosetta. And I got RMSD ~13 Anstrong within each cluster, to me it is very high.

And I'm wondering what's the common range of the RMSD within each cluster, that is acceptable ? (either clustered by Rosetta itself or Calibur)

And what's the algorithm to calculate the distance in the Cluster application of Rosetta?