ADL: Autodock4 problem

Sargis Dallakyan sargis at scripps.edu
Fri Jan 18 10:58:28 PST 2008


> I am trying Autodock4 for flex docking.  When I set up the flexible residues I see that some atom types that are in those residues are not present in the ligand(SA, HD, N).  I added these atoms to be included in the ligand_types list in the grid parameter file.  But when I try to run autogrid4 after adding these atom types it gives me segmentation fault.  Autogrid4 runs fine prior to adding those atom types in the list.  But without running Autogrid4 on those newly added atoms there would be a problem to run Autodock4 that looks for map files for those atoms in flexible residues(SA, HD, and N).  
> Does anyone have any idea about how to go about solving this problem.

I've found why this cause a problem. When you add 'SA' next to ligand_types in 
the grid parameter file, there should be corresponding "map hsg1.SA.map" added 
in gpf as well: http://mgldev.scripps.edu/bugs/show_bug.cgi?id=889


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