[Dock-fans] Combining DOCK with AMBER

[Scott Brozell]

Hi,

On Mon, 29 Oct 2007, Francesco Pietra wrote:

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


http://dock.compbio.ucsf.edu/DOCK_6/6.1/bugfix.2

> 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.


I probably do not understand exactly what you are doing,
why run Dock-prep again ?
Perhaps you should open the amberized receptor files in Chimera:
rec.amber.pdb
rec.prmtop
etc

Scott

> > > 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.