On Mar 7, 2012, at 12:57 AM, Scott Brozell wrote:
So, in short, I am utterly bamboozled. Obviously, antechamber can handle "large multiple residue PDB files", since the Dock Prep tutorial used the AM1-BCC charge model on the large 1ABE.pdb protein, and it worked fine. Why is it not working for me?
No, the receptor charges were assigned using residue matching. See step 1 of http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules... and the chimera dockprep docs: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecontrib.html "Charges for standard residues ... are taken from Amber (details)." Read the force field chapter of the AmberTools manual and references therein for even more details.
Yes, Chimera does not send the entirety of 3GLR to antechamber. Even if that could work, antechamber/sqm is doing a QM charge calculation and would take between hours and days to finish a computation on a system that size. Instead, Chimera uses pre-computed partial charges for standard amino and nucleic acids. For other parts of 3GLR Chimera extracts the parts into Mol2 files and sends them to antechamber for charge assignment (many details glossed over here). I guess my question is why don't you want to just call Dock Prep programatically, as I suggested in my earlier reply? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu