[Dock-fans] Help on sphgen command.

[Teck Maan]

Hi again,
This is the installation detail: 

[tkmaan at roam98-027 Desktop]$ cd dock6/install
[tkmaan at roam98-027 install]$ ./configure gnu
The requested configuration file was found.
The DOCK configuration file has been created.
[tkmaan at roam98-027 install]$ make all
Starting installation of 
DOCK v6.2
at Fri May 16 14:47:50 EDT 2008.

cd ../src && make install
make[1]: Entering directory `/home/tkmaan/Desktop/dock6/src'
cd dock && make install
make[2]: Entering directory `/home/tkmaan/Desktop/dock6/src/dock'
g++ -c  -O2 -o amber_typer.o  amber_typer.cpp
g++ -c  -O2 -o base_grid.o  base_grid.cpp
g++ -c  -O2 -o base_mpi.o  base_mpi.cpp
g++ -c  -O2 -o base_score.o  base_score.cpp
g++ -c  -O2 -o conf_gen.o  conf_gen.cpp
g++ -c  -O2 -o dock.o  dock.cpp
g++ -c  -O2 -o dockmol.o  dockmol.cpp
g++ -c  -O2 -o grid.o  grid.cpp
g++ -c  -O2 -o library_file.o  library_file.cpp
g++ -c  -O2 -o master_score.o  master_score.cpp
g++ -c  -O2 -o orient.o  orient.cpp
g++ -c  -O2 -o score.o  score.cpp
g++ -c  -O2 -o simplex.o  simplex.cpp
g++ -c  -O2 -o sphere.o  sphere.cpp
g++ -c  -O2 -o score_solvent.o  score_solvent.cpp
g++ -c  -O2 -o score_amber.o  score_amber.cpp
g++ -c  -O2 -o sasa.o  sasa.cpp
g++ -c  -O2 -o score_chemgrid.o  score_chemgrid.cpp
g++ -c  -O2 -o utils.o  utils.cpp
g++ -c  -O2 -o trace.o  trace.cpp
cd nab && make all
make[3]: Entering directory `/home/tkmaan/Desktop/dock6/src/dock/nab'
gcc -c -O3 -D_ANSI_SOURCE  molio.c
gcc -c  -O2 -o prm.o  prm.c
make is_LEX_available
make[4]: Entering directory `/home/tkmaan/Desktop/dock6/src/dock/nab'
make[4]: Leaving directory `/home/tkmaan/Desktop/dock6/src/dock/nab'
flex -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex  sff.c
gcc -c  -O2 -o traceback.o  traceback.c
gcc -c  -O2 -o select_atoms.o  select_atoms.c
gcc -c  -O2 -o memutil.o  memutil.c
gcc -c  -O2 -o reslib.o  reslib.c
gcc -c  -O2 -o jacobi.o  jacobi.c
gcc -c  -O2 -o molutil.o  molutil.c
gcc -c  -O2 -o chirvol.o  chirvol.c
gcc -c  -O2 -o regexp.o  regexp.c
gcc -c  -O2 -o binpos.o  binpos.c
gcc -c  -O2 -o time.o  time.c
gcc -c -O3 -D_ANSI_SOURCE  rand2.c
gcc -c -O3 -D_ANSI_SOURCE  conjgrad.c
gcc -c  -O2 -o database.o  database.c
gcc -c  -O2 -o tleap.o  tleap.c
ar rv nab.a molio.o prm.o sff.o traceback.o select_atoms.o memutil.o
reslib.o jacobi.o molutil.o chirvol.o regexp.o binpos.o time.o rand2.o
conjgrad.o database.o tleap.o 
ar: creating nab.a
a - molio.o
a - prm.o
a - sff.o
a - traceback.o
a - select_atoms.o
a - memutil.o
a - reslib.o
a - jacobi.o
a - molutil.o
a - chirvol.o
a - regexp.o
a - binpos.o
a - time.o
a - rand2.o
a - conjgrad.o
a - database.o
a - tleap.o
ranlib nab.a
make[3]: Leaving directory `/home/tkmaan/Desktop/dock6/src/dock/nab'
g++ -O2 -o dock6 amber_typer.o base_grid.o base_mpi.o base_score.o
conf_gen.o dock.o dockmol.o grid.o library_file.o master_score.o
orient.o score.o simplex.o sphere.o score_solvent.o score_amber.o sasa.o
score_chemgrid.o utils.o trace.o nab/nab.a -lm -lpthread 
mv dock6 ../../bin
make[2]: Leaving directory `/home/tkmaan/Desktop/dock6/src/dock'
cd accessories && make install
make[2]: Entering directory `/home/tkmaan/Desktop/dock6/src/accessories'
g77 -c -O2 -fno-automatic -fno-second-underscore -o showbox.o  showbox.f
make[2]: g77: Command not found
make[2]: *** [showbox.o] Error 127
make[2]: Leaving directory `/home/tkmaan/Desktop/dock6/src/accessories'
make[1]: *** [utils] Error 2
make[1]: Leaving directory `/home/tkmaan/Desktop/dock6/src'
make: *** [install] Error 2
[tkmaan at roam98-027 install]$ 

I am using fedora 8. and i tar from the file titled
dock.6.2_source.tar.gz. the sphgen is still not there. Thanks.

Teck Maan

> On Mon, 12 May 2008, Teck Maan Lim wrote:
> 
> > I have DOCK6.2 installed in my fedora
> > 8 machine. I could not find any sphgen or INSPH director in my
> > DOCK6/bin/ directory. All i have is a dock6.exe file in the bin
> > directory. Is my installation wrong? I followed the manual in the
> 
> Probably.
> 
> > following website.
> > http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm
> > 
> > This is the make test that i have run.
> >  
> > Starting validation of 
> > DOCK v6.2
> > at Mon May 12 12:54:55 EDT 2008.
> > 
> > make utils; make dock
> > make[1]: Entering directory `/home/tkmaan/Desktop/dock6/install/test'
> > cd sphere_generation && make test
> > make[2]: Entering directory
> > `/home/tkmaan/Desktop/dock6/install/test/sphere_generation'
> > # Construct sphere set in active site
> > ../../../bin/sphgen
> > make[2]: ../../../bin/sphgen: Command not found
> 
> This confirms that sphgen does not exist.
> Send the details of the installation before testing.
> 
> Scott
> 
> 
>