[Dock-fans] Combining DOCK with AMBER

[Scott Brozell]

Hi,

On Mon, 29 Oct 2007, Francesco Pietra wrote:

> I posted previously that, with DOCK6.1, dock-prep for my protein, after
> repeated fixing, arrived at fractional charges for the residues. Either some
> were still misnamed, or some were lacking. This was the best I could do.
> 
> Accepting the suggestion to go to Amber (someone was even skeptical that the
> fractional charges for this large receptor could be assigned by Antechamber), I
> have now loaded the pdb to leap (Amber9), whereby heavy atoms were added (where
> I had set TER records) and H/lone pairs also added. Both prmtop and inpcrd
> could be saved (and opened correctly with VMD). Of perhaps major concern
> (leap.log attached):
> 
> (Residues lacking connect 0/ connect 1 -
> These don't have chain types marked:
> res  total affected
> CTHR 4
> NSER 4

These are innocuous.  They indicate that some residues are not connected.
And those should correspond to your insertion of TER cards.  See
http://amber.ch.ic.ac.uk/archive/200502/0264.html
http://amber.ch.ic.ac.uk/archive/200505/0290.html

> Should all that be OK, how to go to DOCK now? I have prmtop and inpcrd files
> also for the ligand, obtained from prepare_amber.pl, though, obviously, no such
> files for the complex receptor-ligand.

If prepare_amber.pl was run, there should be all the Amber files (prmtop, etc)
for all three (ligand, receptor, complex).
See step 3 in
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
Once amberization is complete and verified then use step 4 of that tutorial
as a template for creating your own dock input file for rescoring.

> Also, the receptor has 24.000000 charge: should docking be carried out with
> this charged receptor or should it be first neutralized (in leap?).

DOCK's Amber score uses an implicit solvent model in which case
charge neutralization with explicit ions is usually not performed.

Scott

> I realize that this a combination of tricky problems and my limited experience.
> Thanks for your understanding.