[Dock-fans] Combining DOCK with AMBER

[Francesco Pietra]

--- Scott Brozell <sbrozell at scripps.edu> wrote:

> 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

In fact, prepare_amber.pl lig.mol2 rec.pdb produced the expected files, though

mpirun -np 4 dock6.mpi -i dock.in -o dock.out

after the "Initialing MPI Routines for all nodes, said

"getpdb: can't open file 0.amber.pdb"

The dock.out.# don't tell much.

This rec.pdb failed with Dock-prep in Chimera. Again, the program believes that
there are non-standard residue, assigning them to Antechamber, which produces
fractional charges for the residues.

In other words, I did not succeed in getting Chimera and DOCK talking 
together.

Thanks

francesco

 
> 
> > 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.
> 
> 
> 


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