[Dock-fans] dock installation

Syed Tarique Moin tarisyed at yahoo.com
Fri Feb 22 04:14:49 PST 2008


  Hello,
 
 I want to install dock6.1, I have the intel fortran
 compile and i am using suse 10.2 64 bit. 
 
 I made change in the gnu script at this stage 
 FC = ifort, 
 
 then i run ./configure gnu, then i give the command 
 make all and the output is attached here.
 
 Kindly give me suggestion.
 
 Regards 

  > > Starting installation of 
> DOCK v6.1
> at Thu Feb 14 12:02:59 PKT 2008.
> 
> cd ../src && make install
> make[1]: Entering directory `/usr/local/dock6/src'
> cd dock && make install
> make[2]: Entering directory
> `/usr/local/dock6/src/dock'
> cd nab && make
> make[3]: Entering directory
> `/usr/local/dock6/src/dock/nab'
> 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 
> r - molio.o
> r - prm.o
> r - sff.o
> r - traceback.o
> r - select_atoms.o
> r - memutil.o
> r - reslib.o
> r - jacobi.o
> r - molutil.o
> r - chirvol.o
> r - regexp.o
> r - binpos.o
> r - time.o
> r - rand2.o
> r - conjgrad.o
> r - database.o
> r - tleap.o
> ranlib nab.a
> make[3]: Leaving directory
> `/usr/local/dock6/src/dock/nab'
> g++ -O2 -o dock6 amber_typer.o base_mpi.o
> base_score.o conf_gen.o dock.o dockmol.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 nab/nab.a -lm
> -lpthread 
> mv dock6 ../../bin
> make[2]: Leaving directory
> `/usr/local/dock6/src/dock'
> cd accessories && make install
> make[2]: Entering directory
> `/usr/local/dock6/src/accessories'
> ifort -O2 -fno-automatic -fno-second-underscore -o
> showbox showbox.o
> ifort: command line warning #10006: ignoring unknown
> option '-fno-automatic'
> ifort: command line warning #10006: ignoring unknown
> option '-fno-second-underscore'
> ifort -O2 -fno-automatic -fno-second-underscore -o
> showsphere showsphere.o
> ifort: command line warning #10006: ignoring unknown
> option '-fno-automatic'
> ifort: command line warning #10006: ignoring unknown
> option '-fno-second-underscore'
> ifort -O2 -fno-automatic -fno-second-underscore -o
> sphgen sphgen.o
> ifort: command line warning #10006: ignoring unknown
> option '-fno-automatic'
> ifort: command line warning #10006: ignoring unknown
> option '-fno-second-underscore'
> g++ -O2 sphere_selector.cpp -lm -o sphere_selector 
> In file included from
> /usr/include/c++/4.1.2/backward/strstream:51,
> from sphere_selector.cpp:7:
>
/usr/include/c++/4.1.2/backward/backward_warning.h:32:2:
> warning: #warning This file includes at least one
> deprecated or antiquated header. Please consider
> using one of the 32 headers found in section
> 17.4.1.2 of the C++ standard. Examples include
> substituting the header for the header for
> C++ includes, or instead of the
> deprecated header . To disable this
> warning use -Wno-deprecated.
> mv showbox showsphere sphgen sphere_selector
> ../../bin
> sed "s?DOCKHOME?/usr/local/dock6?g" prepare_amber.pl
> > ../../bin/prepare_amber.pl
> sed "s?DOCKHOME?/usr/local/dock6?g" amberize_ligand
> > ../../bin/amberize_ligand
> sed "s?DOCKHOME?/usr/local/dock6?g" amberize_complex
> > ../../bin/amberize_complex
> sed "s?DOCKHOME?/usr/local/dock6?g"
> amberize_receptor > ../../bin/amberize_receptor
> cd ../../bin && chmod +x amberize* prepare_amber.pl
> make[2]: Leaving directory
> `/usr/local/dock6/src/accessories'
> cd gbsa_grids && make install
> make[2]: Entering directory
> `/usr/local/dock6/src/gbsa_grids'
> cd schemgrid_GB && make install
> make[3]: Entering directory
> `/usr/local/dock6/src/gbsa_grids/schemgrid_GB'
> ifort -O2 -fno-automatic -fno-second-underscore
> nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o
> nparmrec.o npolariz.o second.o -o nchemgrid_GB
> ifort: command line warning #10006: ignoring unknown
> option '-fno-automatic'
> ifort: command line warning #10006: ignoring unknown
> option '-fno-second-underscore'
> mv nchemgrid_GB ../../../bin
> make[3]: Leaving directory
> `/usr/local/dock6/src/gbsa_grids/schemgrid_GB'
> cd schemgrid_SA && make install
> make[3]: Entering directory
> `/usr/local/dock6/src/gbsa_grids/schemgrid_SA'
> ifort -O2 -fno-automatic -fno-second-underscore
> nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o
> nparmrec.o npolariz.o nsas.o nsphgrid.o second.o -o
> nchemgrid_SA
> ifort: command line warning #10006: ignoring unknown
> option '-fno-automatic'
> ifort: command line warning #10006: ignoring unknown
> option '-fno-second-underscore'
> mv nchemgrid_SA ../../../bin
> make[3]: Leaving directory
> `/usr/local/dock6/src/gbsa_grids/schemgrid_SA'
> make[2]: Leaving directory
> `/usr/local/dock6/src/gbsa_grids'
> cd grid && make install
> make[2]: Entering directory
> `/usr/local/dock6/src/grid'
> ifort -O2 -fno-automatic -fno-second-underscore
> grid.o score.o score_grid.o gridpoint.o define.o
> io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o
> io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o
> label_node.o label_chem.o label_vdw.o label_flex.o
> mol.o search.o transform.o transformf.o parm.o
> parm_grid.o rotrans.o utility.o vector.o -lm
> -lpthread -o grid 
> ifort: command line warning #10006: ignoring unknown
> option '-fno-automatic'
> ifort: command line warning #10006: ignoring unknown
> option '-fno-second-underscore'
> grid.o: In function `main':
> grid.c:(.text+0x70): multiple definition of `main'
>
/opt/intel/fce/10.1.012/lib/for_main.o:/export/users/nbtester/efi2linuxx86_nightly/branch-10_1/20080112_010000/libdev/frtl/src/libfor/for_main.c:(.text+0x0):
> first defined here
> ld: Warning: size of symbol `main' changed from 56
> in /opt/intel/fce/10.1.012/lib/for_main.o to 1702 in
> grid.o
> /opt/intel/fce/10.1.012/lib/for_main.o: In function
> `main':
>
/export/users/nbtester/efi2linuxx86_nightly/branch-10_1/20080112_010000/libdev/frtl/src/libfor/for_main.c:(.text+0x26):
> undefined reference to `MAIN__'
> make[2]: *** [grid] Error 1
> make[2]: Leaving directory
> `/usr/local/dock6/src/grid'
> make[1]: *** [utils] Error 2
> make[1]: Leaving directory `/usr/local/dock6/src'
> make: *** [install] Error 2
> 


Syed Tarique Moin,
Junior Research Fellow, 
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences, 
University of Karachi, Karachi-75720, Pakistan

tarisyed at yahoo.com
tarisyed at hotmail.com


____________________________________________________________________________________
Never miss a thing. Make Yahoo your home page. 
http://www.yahoo.com/r/hsStarting installation of 
DOCK v6.1
at Thu Feb 14 12:02:59 PKT 2008.

cd ../src && make install
make[1]: Entering directory `/usr/local/dock6/src'
cd dock && make install
make[2]: Entering directory `/usr/local/dock6/src/dock'
cd nab && make
make[3]: Entering directory `/usr/local/dock6/src/dock/nab'
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 
r - molio.o
r - prm.o
r - sff.o
r - traceback.o
r - select_atoms.o
r - memutil.o
r - reslib.o
r - jacobi.o
r - molutil.o
r - chirvol.o
r - regexp.o
r - binpos.o
r - time.o
r - rand2.o
r - conjgrad.o
r - database.o
r - tleap.o
ranlib nab.a
make[3]: Leaving directory `/usr/local/dock6/src/dock/nab'
g++ -O2 -o dock6 amber_typer.o base_mpi.o base_score.o conf_gen.o dock.o dockmol.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 nab/nab.a -lm -lpthread 
mv dock6 ../../bin
make[2]: Leaving directory `/usr/local/dock6/src/dock'
cd accessories && make install
make[2]: Entering directory `/usr/local/dock6/src/accessories'
ifort -O2 -fno-automatic -fno-second-underscore -o showbox showbox.o
ifort: command line warning #10006: ignoring unknown option '-fno-automatic'
ifort: command line warning #10006: ignoring unknown option '-fno-second-underscore'
ifort -O2 -fno-automatic -fno-second-underscore -o showsphere showsphere.o
ifort: command line warning #10006: ignoring unknown option '-fno-automatic'
ifort: command line warning #10006: ignoring unknown option '-fno-second-underscore'
ifort -O2 -fno-automatic -fno-second-underscore -o sphgen sphgen.o
ifort: command line warning #10006: ignoring unknown option '-fno-automatic'
ifort: command line warning #10006: ignoring unknown option '-fno-second-underscore'
g++ -O2 sphere_selector.cpp -lm -o sphere_selector 
In file included from /usr/include/c++/4.1.2/backward/strstream:51,
from sphere_selector.cpp:7:
/usr/include/c++/4.1.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated header . To disable this warning use -Wno-deprecated.
mv showbox showsphere sphgen sphere_selector ../../bin
sed "s?DOCKHOME?/usr/local/dock6?g" prepare_amber.pl > ../../bin/prepare_amber.pl
sed "s?DOCKHOME?/usr/local/dock6?g" amberize_ligand > ../../bin/amberize_ligand
sed "s?DOCKHOME?/usr/local/dock6?g" amberize_complex > ../../bin/amberize_complex
sed "s?DOCKHOME?/usr/local/dock6?g" amberize_receptor > ../../bin/amberize_receptor
cd ../../bin && chmod +x amberize* prepare_amber.pl
make[2]: Leaving directory `/usr/local/dock6/src/accessories'
cd gbsa_grids && make install
make[2]: Entering directory `/usr/local/dock6/src/gbsa_grids'
cd schemgrid_GB && make install
make[3]: Entering directory `/usr/local/dock6/src/gbsa_grids/schemgrid_GB'
ifort -O2 -fno-automatic -fno-second-underscore nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o second.o -o nchemgrid_GB
ifort: command line warning #10006: ignoring unknown option '-fno-automatic'
ifort: command line warning #10006: ignoring unknown option '-fno-second-underscore'
mv nchemgrid_GB ../../../bin
make[3]: Leaving directory `/usr/local/dock6/src/gbsa_grids/schemgrid_GB'
cd schemgrid_SA && make install
make[3]: Entering directory `/usr/local/dock6/src/gbsa_grids/schemgrid_SA'
ifort -O2 -fno-automatic -fno-second-underscore nchemgrid.o dist.o nddist.o ndconst.o ngrdout.o nparmrec.o npolariz.o nsas.o nsphgrid.o second.o -o nchemgrid_SA
ifort: command line warning #10006: ignoring unknown option '-fno-automatic'
ifort: command line warning #10006: ignoring unknown option '-fno-second-underscore'
mv nchemgrid_SA ../../../bin
make[3]: Leaving directory `/usr/local/dock6/src/gbsa_grids/schemgrid_SA'
make[2]: Leaving directory `/usr/local/dock6/src/gbsa_grids'
cd grid && make install
make[2]: Entering directory `/usr/local/dock6/src/grid'
ifort -O2 -fno-automatic -fno-second-underscore grid.o score.o score_grid.o gridpoint.o define.o io.o io_grid.o io_gridf.o mol_prep.o io_receptor.o io_mol2.o io_pdb.o io_ptr.o io_sph.o label.o label_node.o label_chem.o label_vdw.o label_flex.o mol.o search.o transform.o transformf.o parm.o parm_grid.o rotrans.o utility.o vector.o -lm -lpthread -o grid 
ifort: command line warning #10006: ignoring unknown option '-fno-automatic'
ifort: command line warning #10006: ignoring unknown option '-fno-second-underscore'
grid.o: In function `main':
grid.c:(.text+0x70): multiple definition of `main'
/opt/intel/fce/10.1.012/lib/for_main.o:/export/users/nbtester/efi2linuxx86_nightly/branch-10_1/20080112_010000/libdev/frtl/src/libfor/for_main.c:(.text+0x0): first defined here
ld: Warning: size of symbol `main' changed from 56 in /opt/intel/fce/10.1.012/lib/for_main.o to 1702 in grid.o
/opt/intel/fce/10.1.012/lib/for_main.o: In function `main':
/export/users/nbtester/efi2linuxx86_nightly/branch-10_1/20080112_010000/libdev/frtl/src/libfor/for_main.c:(.text+0x26): undefined reference to `MAIN__'
make[2]: *** [grid] Error 1
make[2]: Leaving directory `/usr/local/dock6/src/grid'
make[1]: *** [utils] Error 2
make[1]: Leaving directory `/usr/local/dock6/src'
make: *** [install] Error 2




Syed Tarique Moin,
Junior Research Fellow, 
H.E.J. Research Institute of Chemistry,
International Center for Chemical and Biological Sciences, 
University of Karachi, Karachi-75720, Pakistan

tarisyed at yahoo.com
tarisyed at hotmail.com
       
---------------------------------
Never miss a thing.   Make Yahoo your homepage.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080222/c1a68fa9/attachment-0001.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: install.log
Type: text/x-log
Size: 5525 bytes
Desc: pat1978063294
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20080222/c1a68fa9/attachment-0001.bin 


More information about the Dock-fans mailing list