[Dock-fans] DOCK 6.2 installation

hannah pamela tan hpdiamantetan at yahoo.com
Sun May 31 03:12:58 PDT 2009


Dear Sir,
 
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:
 
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
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)
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
 
 
asking again for your help.. thanks
 
Hannah
 
 
Hannah Pamela D. Tan
BS Chemistry Student
Institute of Chemistry
University of the Philippines Los Baños
Laguna, Philippines


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