[Dock-fans] DOCK 6.2 installation

Scott Brozell sbrozell at rci.rutgers.edu
Sun May 31 15:43:09 PDT 2009


Hi,

On Sun, May 31, 2009 at 03:12:58AM -0700, hannah pamela tan wrote:
>  
> This is again about the DOCK 6.2 installation. Before I applied the corrections you sent for the src folder files, this is what showed up in the cygwin terminal:
>  


I didnt see any suggested corrections.

> edwin at ADMIN-CA1D9FF92 /cygdrive/c
> $ cd dock6/install
>  
> edwin at ADMIN-CA1D9FF92 /cygdrive/c/dock6/install
> $ ./configure gnu
> The requested configuration file was found.
>  
> Warning: the configuration file already exists with the creation stamp:
> # Created at Tue May 26 00:31:31  2009 via ./configure sgi
> It will be overwritten !
> Don't forget to make clean before rebuilding.
> The best way to reconfigure and rebuild is to start with make distclean.
> Reconfiguring after make distclean will avoid this warning.
>  
> The DOCK configuration file has been created.
>  
> edwin at ADMIN-CA1D9FF92 /cygdrive/c/dock6/install
> $ make all # builds all the DOCK programs


Before this step, you should have heeded the suggestion above and ran:
% make clean

> Starting installation of
> DOCK v6.2
> at Sat May 30 10:31:22  2009.
>  
> cd ../src && make install
> make[1]: Entering directory `/cygdrive/c/dock6/src'
> cd dock && make install
> make[2]: Entering directory `/cygdrive/c/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
> score.cpp: In method `class string Energy_Score::output_score_summary(float)':
> score.cpp:282: `fixed' undeclared (first use this function)
> score.cpp:282: (Each undeclared identifier is reported only once
> score.cpp:282: for each function it appears in.)
> make[2]: *** [score.o] Error 1
> make[2]: Leaving directory `/cygdrive/c/dock6/src/dock'
> make[1]: *** [dock6] Error 2
> make[1]: Leaving directory `/cygdrive/c/dock6/src'
> make: *** [install] Error 2
>  
>  
> I tried to apply the corrections for the score.cpp file (adding #include <string.h>) and this was the result after trying to build the executable(s) – the same error was detected in the score.cpp file:
>  
>  
> edwin at ADMIN-CA1D9FF92 /cygdrive/c/dock6/install
> $ make all # builds all the DOCK programs
> Starting installation of
> DOCK v6.2
> at Sat May 30 10:36:19  2009.
>  
> cd ../src && make install
> make[1]: Entering directory `/cygdrive/c/dock6/src'
> cd dock && make install
> make[2]: Entering directory `/cygdrive/c/dock6/src/dock'
> g++ -c  -O2 -o score.o  score.cpp
> score.cpp: In method `class string Energy_Score::output_score_summary(float)':
> score.cpp:284: `fixed' undeclared (first use this function)
> score.cpp:284: (Each undeclared identifier is reported only once
> score.cpp:284: for each function it appears in.)
> make[2]: *** [score.o] Error 1
> make[2]: Leaving directory `/cygdrive/c/dock6/src/dock'
> make[1]: *** [dock6] Error 2
> make[1]: Leaving directory `/cygdrive/c/dock6/src'
> make: *** [install] Error 2
>  
>  
> Well, to try again, I applied all the corrections you gave to all the files concerned (amber_typer.cpp ; conf_gen.cpp ; dockmol.cpp ; library_file.cpp ; orient.cpp ; score.cpp ; simplex.cpp ; sphere.cpp ; utils.cpp ) and, still, the same error was detected in the score.cpp file.
>  
>  
> edwin at ADMIN-CA1D9FF92 /cygdrive/c/dock6/install
> $ make all # builds all the DOCK programs
> Starting installation of
> DOCK v6.2
> at Sat May 30 10:53:09  2009.
>  
> cd ../src && make install
> make[1]: Entering directory `/cygdrive/c/dock6/src'
> cd dock && make install
> make[2]: Entering directory `/cygdrive/c/dock6/src/dock'
> g++ -c  -O2 -o amber_typer.o  amber_typer.cpp
> g++ -c  -O2 -o conf_gen.o  conf_gen.cpp
> g++ -c  -O2 -o dockmol.o  dockmol.cpp
> g++ -c  -O2 -o orient.o  orient.cpp
> g++ -c  -O2 -o score.o  score.cpp
> score.cpp: In method `class string Energy_Score::output_score_summary(float)':
> score.cpp:284: `fixed' undeclared (first use this function)

So in all cases there is an error on `fixed' undeclared.
If you enter the error into the search dock fans box:
http://dock.compbio.ucsf.edu/DOCK_6/index.htm#searchdockfans
then a number of useful threads are found which indicate that your
g++ compiler is really really old:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-May/001624.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-October/001245.html

In summary do this:
download and install a recent g++ compiler (4.1 has been heavily used by me)
and verify that it is in your path ( g++ -v );
cd dock6/install
make distclean
./configure gnu
make install

Scott



More information about the Dock-fans mailing list