[Dock-fans] Combining DOCK with AMBER

Wed Oct 31 02:03:29 PDT 2007

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

> 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

OK, thanks. However, reminding for installations where MPICH points to OpenMpi,
to proceed as follows:

MPICH_HOME='/usr/loc' (or other appropriate location)
export MPICH_HOME
cd install
make clean
make dock # builds only the dock program

(otherwise errors arise about MPICH)

Now amber_score with option "ligand" 

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

produced in a few minutes the expected files.

> 
> 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

That did not succeed (assuming that I kave implemented correctly the
suggestion, which should be verified)

I created a directory, copying in the prmtop and inpcrd file for the receptor
as obtained from LEAP (just the files that worked out perfectly for
amber_score). Dock-prep (from Chimera, accepting defaults, i.e. everything
selected except "Delete non complexed ions", and considering H-bonds, reported
errors "Value error: underlying C++ Molecule object is missing", which is
documented in the attacher error.log. 

However, the error is different from that obtained with the pdb file created
from the above prmtop and inpcrd using "ambpdb" of Amber9. In the latter case,
apparently, some standard amino acid was erroneously taken by Dock-Prep as
non-standard residue and passed to Antechamber, which failed to do correctly,
reporting fractional charges for the residue. For the present protein, the
relevant window that was presented, was

ASH+ALA+ASN  +0
ASH+ALA+PRO +0
ASH+GLY+MET +0
GLH+ALA++ALA +0
GLH+ARG++LEU +1
GLH+ARG+THR +0

accepting that, fractional charges were calculated for the residues. Any change
to the values (+0 or +1) presented led to crashing.

What I was trying was to run some simple docking before amber_score. The
tutorial passed without problems. Even my protein passes correctly Dock-prep,
if prepare from Chimera is accepted, and I could run all dockings as in the
tutorial. However, the protein handled by Chimera is not accepted by Amber9 or
amber_score.

Thanks

francesco

> > > 
> > > 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 
> 
> -- 
> 
> 

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: error.log.tar.bz2
Type: application/x-bzip
Size: 1615 bytes
Desc: 2194036910-error.log.tar.bz2
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071031/bfa25e14/attachment.bin 