[Dock-fans] Combining DOCK with AMBER

[Francesco Pietra]

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

> 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

Ah! I failed to look at dock-fans. Sorry. However, the edited file (attached
base_mpi.cpp) gives the same error (getpdb: can't open file 0.amber.pdb) as the
original file (attached original_base_mpi.cpp).

Probably I was unable to follow the recipe, and there is no one around here
capable of C or C++. I simply deleted a line of program from the original file.

I have checked that the prmtop and inpcrd files generated by prepare_amber.pl
produce the correct representation in both VMD and Chimera.


> 
> > 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 ?

It was to check if the pdb fixed by LEAP was now OK for DockPrep. It was not.

Thanks
francesco

> 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.
> 
> 


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