Recently I requested a copy of HADDOCK from Dr. Alexandre Bonvin in order to generate some docked dimers for my colleagues. They are working on some dimeric proteins but they have no idea how to obtain the dimeric conformation from homologous known structures.
I spent few days reading the threads in the HADDOCK discussion group at Yahoo and I have made the HADDOCK 2.1 work well on my iMac. Here is the system environment I used:
iMac: 3.06GHz Intel i3 CPU
OS: 10.6. 5
1. Always change the toppar files from 5.3 (default in run.cns) to 5.4 (must be 5.4 if you use CNS 1.3).
2. The path of CNS in run.cns is probably not same as your own. Always modify it before run HADDOCK
3. Numbers of CPUs used for calculation are 2 by default, it’s changeable,too.
I use the AIR restraint file to generate a dimeric structure. The results generated by HADDOCK and Modeller are showing here.
The HADDOCK and Modeller generated dimer conformations are colored in orange and blue, respectively.