[Chimera-users] [Dock-fans] Help with antechamber
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
>> "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
> and the chimera dockprep docs:
> "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?
UCSF Computer Graphics Lab
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