[Dock-fans] Installing DOCK6.5

William Joseph Allen william.joseph.allen at gmail.com
Fri Nov 2 07:42:57 PDT 2012


Hi Calvin,

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,

Joe Allen



On Fri, Nov 2, 2012 at 9:12 AM, Calvin F. Cahall
<calvin.cahall at centre.edu>wrote:

> Joe,
> 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
> make[2]: *** [amberdock] Error 2
> make[1]: *** [timed_test] Error 2
> make: *** [test] Error 2
>
> Could these be errors from the deleting the -fno-automatic? or should I
> continue to try to complete the chimera tutorials?
>
> Again, thank you so much!
> Calvin
> ________________________________
> From: William Joseph Allen [william.joseph.allen at gmail.com]
> Sent: Wednesday, October 31, 2012 11:15 AM
> To: Calvin F. Cahall; dock-fans at docking.org
> Subject: Re: [Dock-fans] Installing DOCK6.5
>
> 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
>
> Any suggestions would be greatly appreciated. Thanks!
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org<mailto:Dock-fans at docking.org><mailto:
> Dock-fans at docking.org<mailto:Dock-fans at docking.org>>
> http://mailman.docking.org/mailman/listinfo/dock-fans
>
>
>
> --
> William Joseph Allen, Ph.D.
> Robert C. Rizzo Research Group
> Department of Applied Mathematics and Statistics
> Stony Brook University
> http://ringo.ams.sunysb.edu/~wjallen/<
> http://ringo.ams.sunysb.edu/%7Ewjallen/>
>
>
>
>
> --
> William Joseph Allen, Ph.D.
> Robert C. Rizzo Research Group
> Department of Applied Mathematics and Statistics
> Stony Brook University
> http://ringo.ams.sunysb.edu/~wjallen/<
> http://ringo.ams.sunysb.edu/%7Ewjallen/>
>
>
>
>
> --
> William Joseph Allen, Ph.D.
> Robert C. Rizzo Research Group
> Department of Applied Mathematics and Statistics
> Stony Brook University
> http://ringo.ams.sunysb.edu/~wjallen/
>
>


-- 
William Joseph Allen, Ph.D.
Robert C. Rizzo Research Group
Department of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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