[Dock-fans] Combining DOCK with AMBER

[Scott Brozell]

Hi,

On Tue, 30 Oct 2007, Francesco Pietra wrote:

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


base_mpi.cpp has been correctly patched.  Reinstall dock:
cd install; make dock

Scott

> > > 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.
> > 
> > 
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 

--