[Dock-fans] question about sphgen and dock6

gaojun gaojun at tongji.edu.cn
Sat Jul 6 07:05:47 PDT 2013

Hello dock-fans:

    I am a new dock6 user, and I got a question recently. 

    I treated the atoms within the distance to 10A to a ligand as the binding site, and produced the ms/sph files  with dms/sphere_cpp respectively. The box file is produced directly according to the binding site, but not to the sph file. At the docking stage, a sph file is need as one input parameter. My question is : the box file and grid file are produced according to the binding site atoms, so the sph file can be omitted? or clustering is not needed anymore for the sph file?

    My second question is :  On my server, for a protein and a small molecular, sphgen_cpp runs very slow, but dock6 runs very fast. Is it right?

    Thanks to all dock-fans! 


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