UNRES-dock download and compilation:
UNRES-dock is an extension of UNRES package, which allows to run protein-protein and protein-peptide docking simulations using MREMD simulations. Downloading and compilation of the tools is the same as for regular UNRES package. Alternatively, use UNRES-dock server at: http://unres-server.chem.ug.edu.pl.


UNRES-dock procedure:
1. Generation of initial structures of the complex
2. MREMD simulations
3. WHAM analysis
4. Cluster analysis
5. Reconstruction of representative structures to all-atom ones

Modify top lines in prepare_all.csh file and execute it to generate input files for points 1-4. To use different pdb files, simply modify the variables in prepare_all.csh file.
Submit jobs to run points 2-4 and then reconstruct the structures using cluster2allatom.csh on the *_ave.pdb file obtained from cluster analysis (point 5). Please note, that all-atom reconstruction uses pulchra tool (http://cssb.biology.gatech.edu/skolnick/files/PULCHRA/index.html), which has to be installed.