ADL: Flexible bb docking for the receptor in autodock

Jianmin Meng jianmin.meng at umassmed.edu
Wed Mar 5 09:19:08 PST 2008


Hi,

When I set up autodock with flexible residues on the receptor, only the side
chain is flexible.  Does anyone know how to set up autodock for fexible bb
docking as well?

Also, it seems to me autodock can only accommodate 10 residues as flexible
residues, and it stops working when I set up the flexible residues to ~15 aa
even though the maximum torsion is well below 32 as allowed by default.  Do
I need to change some parameter and recompile the program?

I also have some strange experience concerning Pro.  In one instance, it's
OK to include Pro in flexible file, but in others, I have to exclude Pro
from the flexible receptor file in order for autodock to work.  Anybody has
any clue?

In addition, it does not seem to work if I set up the flexible receptor file
as non-consecutive residues (e.g., 5-10, 15-18).  Does the flexible residue
has to be connected to each other or there's some setting that I'm not aware
of that can be changed?

Thanks ahead for your time and help!

Jianmin





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