[Dock-fans] Help on sphgen command.

[Alessandro Nascimento]

> make[2]: g77: Command not found

You need to have a g77 fortan compiler in order to have all dock
accessories programs running properly.
Specifically, sphgen is written in fortran and requires g77.
Since you're running Fedora, it should be easy to get g77 using yum!

hope this helps,

--alessandro

On Fri, May 16, 2008 at 11:53 AM, Teck Maan <teck.m.lim at wmich.edu> wrote:
>
> 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
>>
>>
>>
>
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