My software notes

March 29, 2011

HADDOCK on iMac and a quick benchmark

Filed under: softwares and scripts,xplor/xplor-nih/cns — kpwu @ 11:52 am
Tags: ,

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
CNS: 1.3

Quick notes:

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 best 10 structures are superimposed.

The HADDOCK and Modeller generated dimer conformations are colored in orange and blue, respectively.

blue is from Haddock and orange is from Modeller 9v8


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