Docking

Dear all,

I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.

First, I extracted the top 10% by sorting the I_sc with:

sort -n -k2 example_score_file.sc | head -n 1000 | awk '{print $2 "\t" $25 "\t" $NF}' > score_I-sc_tag.dat

Dear Rosetta Users, 

I'm going to run a molecular docking simulation of a tripeptide - small protein (around 150 aminoacids) complex.
The tripeptide consists of all D-amino acids and has about 20 rotatable bonds. 

Which application -- between RosettaLigand and FlexPepDock -- is better to dock such a small and high-flexible peptide ?
Moreover, I'd like to know which is the most up-to-date protocol to incorporate non-canonical amino acids into Rosetta.

Thanks in advance!
Samuele  

Hello all,

To perform the Flex-pep-docking protocol (ab-initio mode), I need to create fragment files for the target peptide (with 8 residues). I have tried to do this with the make-fragment.pl script . However, I get the attached error. I have already installed the last version of Blast tools. please let me know what is the problem and how it can be solved?

Hello,

I am performing Rosetta ligand docking and I generated the .params file for the ligand with molfile_to_params.py file. I was wondering whether the partial charges in the .params file generated in this way are reliable. Or do I need to do DFT calculation or use another method to get the correct partial charges? 

Any suggestion is appreciated.

P.S: I obtained the ligand pdb file from rcsb and then convert it to sdf file. Then I generated the conformers with BCL and finally use molfile_to_params.py.