Docking

Hi,

I have recently used the Docking2 program for refining my docked models (job IDs 22582 and 22583). The first has failed due to some problem in the prepacking stage while for the second one the job was finished. For the first one it appears that there was some error in the input file.  The latter although the job has finished it is showing a different error ' 

Hi everybody,

I am trying to run on the server some docking2 tests between two known interacting proteins. In fact, I would like to explore a situation including as part of the interacting interface a ligand that is often observed in 3D structures of homologs at a site contributed by the two partners. However, when I launch jobs with ligand coordinates at its final site included in the pdb of the first partner, the simulation fails and I receive an error message.

Hi All:

I am following the tutorial post on this page (http://faculty.washington.edu/dimaio/wordpress/software/).

In the tutorial, they are using one script named "denovo_density.macosclangrelease" which I cannot find it in Rosetta 3.5 . So I wonder do I need to update the latest version of Rosetta or the script they used is not public available.

Many thanks,

Xiaodi

Hello Friends

I am trying to run a global docking search on two proteins on the university computing cluster sampling 100K structures.

docking_protocol.mpi.linuxgccrelease -database /home/aaj30/rosetta_src_2015.39.58186_bundle/main/database -s xyz.pdb -use_input_sc -ex1 -ex2aro -nstruct 100000 -randomize1 -randomize2 -dock_pert 5 10 -spin