[Chimera-users] [Dock-fans] Help with antechamber

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 7 10:04:37 PST 2012

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.htm
> 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 Pettersen
                         UCSF Computer Graphics Lab

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