[Dock-fans] Installing DOCK6.5

Scott Brozell sbrozell at rci.rutgers.edu
Mon Nov 5 23:12:19 PST 2012


Hi,

> > Error from amberize_ligand; the name of the ligand is

This is a FAQ:
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#Error%20from%20amberize_ligand;

scott

On Fri, Nov 02, 2012 at 10:42:57AM -0400, William Joseph Allen wrote:
> 
> I'm not sure what is causing those errors, but it appears to be localized
> to the amberscore module. When running DOCK, you may never even use
> amberscore considering the plethora of scoring functions that are already
> available, or will be coming out in the DOCK 6.6 release:
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Scoring
> I would recommend moving on to the Chimera tutorial and on to DOCK. Good
> luck,
> 
> On Fri, Nov 2, 2012 at 9:12 AM, Calvin F. Cahall
> > I proceeded to make test and I seemed to receive more PASSED tests than
> > possible FAILURE. However, these were the errors I received at the end of
> > the "make test".
> >
> > Error from amberize_ligand; the name of the ligand is
> >     ASL
> >     Examine amberize_ligand.lig.1.out
> >
> > make[3]: *** [amberize] Error 3
> >
> > Could these be errors from the deleting the -fno-automatic? or should I
> > continue to try to complete the chimera tutorials?
> >
> > From: William Joseph Allen [william.joseph.allen at gmail.com]
> > Hi Calvin,
> >
> > I'm glad that worked, my advice is to proceed with "make tests", or you
> > can just try running the main dock executable:
> >
> > ./bin/dock6
> >
> > too see if you get the DOCK welcome message. You can ignore most of the
> > "warning" messages that the build will print to screen, what you are really
> > interested in seeing is whether there were any "error" messages. But if
> > there are none, then I would say you are good to go.
> >
> > Joe Allen
> >
> >
> >
> >
> > On Wed, Oct 31, 2012 at 9:33 AM, Calvin F. Cahall <
> > calvin.cahall at centre.edu<mailto:calvin.cahall at centre.edu>> wrote:
> > Joe,
> >
> > I greatly appreciate all of your suggestions and your thorough
> > explanations. Before I read your second email I tried manually deleting the
> > "-fno-automatic" before using the make command. This time was the first
> > time that the DOCK installation was completed and I also have multiple
> > executable files in my bin folder, where any other time, only the dock
> > executable was present. However, looking through what was returned in the
> > terminal i received a large number of messages such as:
> > parmrec.f:267: warning: will never be executed
> > or
> > lapack.F:2009: warning: will never be executed.
> > So my question now is, should I try running DOCK and moving through the
> > tutorials as is? Or would you recommend trying to resolve my errors with
> > the g77 compiler using suggestions that you have given me?
> >
> > Again, thank you very much for all of your help.
> > Calvin
> > ________________________________
> > From: William Joseph Allen [william.joseph.allen at gmail.com<mailto:
> > william.joseph.allen at gmail.com>]
> > Sent: Monday, October 29, 2012 3:06 PM
> > To: Calvin F. Cahall
> > Cc: dock-fans at docking.org<mailto:dock-fans at docking.org>
> > Subject: Re: [Dock-fans] Installing DOCK6.5
> >
> > Hi Calvin,
> >
> > I see now your previous messages on the mailing list. I am curious, what
> > steps did you take to install g77? You can confirm whether it is installed
> > by typing "which g77" or "g77 --version" on the command line. I would have
> > installed g77 by typing "sudo apt-get install g77" on the command line, is
> > this what you did?
> >
> > The error that I see in that previous e-mail (using g77) may have to do
> > with the "-static" flag you added in the config.h file. From what I
> > understand, that option won't work unless the libraries it is looking for
> > have also been compiled with the "-static" flag. My biggest concern here is
> > that the compiler is trying to link to a library it can't find. I am
> > running OS 10.4 on my mac, and I had to install X11 at some point for the
> > extra libraries. But from what I understand, Macs that came with 10.7 or
> > newer already should have X11 libs installed, but I'm not sure where they
> > are or if the g77 compiler knows how to link to them. I believe you can
> > give the g77 compiler a flag like -L/usr/lib/X11/ to specify a specific
> > path for a library it can't find.
> >
> > If I were you, I would start fresh. Make sure g77 is installed. Go into
> > the ~/dock6/install directory and type "make clean" then "./configure gnu".
> > Go into the resulting config.h file and make sure the compiler scheme is
> > gcc / g++ / g77, and make sure you have each of those installed by typing
> > "which gXX" or "gXX --version" on the command line.
> >
> > Finally, type "make" and post any output to this e-mail. I will try to
> > help as much as I can, but my unfamiliarity with OS 10.8 may be a handicap.
> > Also, I may lose power at any moment due to this hurricane, so it could
> > take me a while to respond.
> >
> > Joe Allen
> >
> >
> >
> > On Mon, Oct 29, 2012 at 2:31 PM, William Joseph Allen <
> > william.joseph.allen at gmail.com<mailto:william.joseph.allen at gmail.com
> > ><mailto:william.joseph.allen at gmail.com<mailto:
> > william.joseph.allen at gmail.com>>> wrote:
> > Hi Calvin,
> >
> > For future reference, if the "make" command ends with errors (as it did
> > according to that output), then there is no point in trying "make test",
> > because it is sure to fail.
> >
> > From reading what you cut-and-paste into the e-mail, I see that the
> > specific error it crashed on was "f951: error: unrecognized command line
> > option "-fno-automatic"".
> >
> > I am not really familiar with the g95 compiler, but apparently
> > "-fno-automatic" is not an option it will take. If you look in your
> > config.h file in your ~/dock6/install directory, you will see a line that
> > says "FFLAGS=      -O2 -fno-automatic -fno-second-underscore"
> >
> > These are flags that are passed to the fortran compiler. One thing you
> > could try is to modify that line and manually remove the "-fno-automatic"
> > flag, and try to recompile. But to be honest, I have no idea what effect
> > that will have on the compile, so maybe some extra digging into what that
> > flag does, and what an equivalent flag for the g95 compiler is would be
> > prudent.
> >
> > I have installed dock 6.5 on my macbook previously, using the gcc / g++ /
> > g77 compilers previously, so I'm not sure what your error was with g77. I
> > am running a pretty old OS (10.4), however, so maybe there is some issue
> > that I am unaware of with the newer OS. If you have the output of the
> > "make" command using the g77 compiler, I would be happy to look at that to
> > see if I see any red flags.
> >
> > Joe Allen
> >
> >
> >
> >
> > On Mon, Oct 29, 2012 at 2:16 PM, Calvin F. Cahall <
> > calvin.cahall at centre.edu<mailto:calvin.cahall at centre.edu><mailto:
> > calvin.cahall at centre.edu<mailto:calvin.cahall at centre.edu>>> wrote:
> > Hello,
> >
> > I am having quite a time getting this program installed successfully on my
> > Mac. I have tried a number of suggestions from replies here and some seemed
> > to fix some of the errors. I have tried switching from g77 to g95. I have
> > also installed the flex package on my computer using MacPorts. I was having
> > linking problems and also had an error 127 after the make test command
> > before these changes were made. After doing these, I don't think I have any
> > linking problems but the error 127 is still present when i use make test.
> > Also, before trying to re-install after making changes, I delete the old
> > files and perform make clean and make realclean commands.
> >
> > Starting installation of
> > DOCK v6.5
> > at Mon Oct 29 13:47:50 EDT 2012.
> >
> > cd ../src && make install
> > cd dock && make install
> > g++ -c  -O2 -o filter.o  filter.cpp
> > 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 score_descriptor.o  score_descriptor.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
> > gcc -c -O3 -D_ANSI_SOURCE  molio.c
> > gcc -c  -O2 -o prm.o  prm.c
> > prm.c: In function ‘writeparm’:
> > prm.c:1571: warning: embedded ‘\0’ in format
> > make is_LEX_available
> > flex -t mm_options.l | sed 's/yy/mmo/g' > lex.mm_options.c
> > gcc -c -O3 -D_ANSI_SOURCE -DDOCK -Dflex  sff.c
> > sff.c: In function ‘checkpoint’:
> > sff.c:734: warning: embedded ‘\0’ in format
> > sff.c: In function ‘mm_set_checkpoint’:
> > sff.c:1615: warning: incompatible implicit declaration of built-in
> > function ‘strdup’
> > gcc -c  -O2 -o traceback.o  traceback.c
> > traceback.c: In function ‘rt_errormsg’:
> > traceback.c:14: warning: format not a string literal and no format
> > arguments
> > traceback.c:14: warning: format not a string literal and no format
> > arguments
> > gcc -c  -O2 -o select_atoms.o  select_atoms.c
> > gcc -c  -O2 -o memutil.o  memutil.c
> > memutil.c: In function ‘vector’:
> > memutil.c:31: warning: format ‘%lld’ expects type ‘long long int’, but
> > argument 3 has type ‘size_t’
> > memutil.c:31: warning: format ‘%lld’ expects type ‘long long int’, but
> > argument 3 has type ‘size_t’
> > 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 archive 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
> > g++ -O2 -o dock6 filter.o 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 score_descriptor.o simplex.o sphere.o
> > score_solvent.o score_amber.o sasa.o score_chemgrid.o utils.o trace.o
> > nab/*.o -lm -lpthread
> > mv dock6 ../../bin
> > cd accessories && make install
> > g95 -c -O2 -fno-automatic -fno-second-underscore -o showbox.o  showbox.f
> > f951: error: unrecognized command line option "-fno-automatic"
> > make[2]: *** [showbox.o] Error 1
> > make[1]: *** [utils] Error 2
> > make: *** [install] Error 2
> >
> > And this is the end of what is returned from make test:
> >
> > cd bump_filter && make test
> > cd ../grid_generation && make test
> > # Construct box to enclose spheres
> > ../../../bin/showbox < box.in<http://box.in><http://box.in> > /dev/null
> > /bin/sh: ../../../bin/showbox: No such file or directory
> > make[4]: *** [showbox] Error 127
> > make[3]: *** [grid_generation] Error 2
> > make[2]: *** [sampling] Error 2
> > make[1]: *** [timed_test] Error 2
> > make: *** [test] Error 2
> >


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