[Dock-fans] Running interactive mode tutorials

[Francesco Pietra]

--- Francis E Reyes <Francis.Reyes at Colorado.EDU> wrote:

> Does vdw.defn exist? Does it exist on all nodes?

/usr/local/dock6/parameters/vdw_AMBER_parm99.defn

which file is rw-r--r-- francesco francesco
________________
Then, I edited manually rigid.in (attached) and tried both parallel and serial


dock6.mpi -i dock.in -o dock.out

dock6 -i dock.in -o dock.out

getting same error:
Could not open vdw.defn for reading.

dock.out from serial command is also attached.
______________________
This

/usr/local/dock6/parameters/vdw_AMBER_parm99.defn

found no problems in "grid.in", tutorial "Generating the grid"


francesco


> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> 
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
> 
> 
> 
> On Oct 7, 2007, at 11:22 AM, Francesco Pietra wrote:
> 
> > I fear I am misunderstanding both tutorials and manual about  
> > commands in
> > interactive mode.
> >
> > Using Dock6.1, I was unable to run interactively "Generating the  
> > Grid" tutorial
> > with command (grid.in nonexistent):
> >
> > grid -i grid.in -o grid.out -s
> >
> > By providing a hand generated grid.in with correct paths, the  
> > computation
> > completed successfully in 13 min.
> > ________
> >
> > Similarly, I was unable to run Docking tutorial with command  
> > (nonexistent
> > dock.in file):
> >
> > mpirun -np 4 dock6.mpi -i dock.in
> >
> > Error: DOCK must be run with the -o outfile option under MPI
> >
> > Then, I tried:
> >
> > mpirun -np 4 dock6.mpi -i dock.in -o dock.out
> >
> > Initialing MPI Routines (for each cpu)
> > and  getting immediately four output files:
> >
> > dock.out : Could not open vdw.defn.
> >
> > Same problem with dock.out.# (# = 1, 2, 3)
> >
> > Because the tutorial suggests to first generate the in file  
> > interactively in
> > view of heavy computations (my task), I am asking for help about my  
> > puzzle.
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> > ______________________________________________________________________ 
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> 
> 



       
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