[Dock-fans] Dock-fans Digest, Vol 60, Issue 24

Prashant Kumar prashantkbio at gmail.com
Thu May 28 03:18:46 PDT 2009


Dear Pasha,
                    Use sphgen_cpp. You can find it on UCSF-DOCK web site.

On Thu, May 28, 2009 at 2:21 PM, <dock-fans-request at docking.org> wrote:

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> Today's Topics:
>
>   1. SPHGEN error (pasha shak)
>   2. dock 6.2 installation (hannah pamela tan)
>   3. dock 6.2 installation (hannah pamela tan)
>   4. dock 6.2 installation (hannah pamela tan)
>   5. problem g77 using ubuntu 9.04 and headers missing for     dock
>      executables (Davide Mercadante)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 May 2009 22:30:12 -0700 (PDT)
> From: pasha shak <pasha_shak at yahoo.com>
> Subject: [Dock-fans] SPHGEN error
> To: dock-fans at docking.org
> Message-ID: <804979.8401.qm at web50401.mail.re2.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi All,
> SPHGEn generates the following error,
>
>
> fmt: read unexpected character
> apparent state: internal I/O last format:
> (A3,I3,A1,2X,A4,1X,F7.3,2F9.3,1X,A3,7X,3F7.3)
> lately reading sequential formatted internal IO
> Aborted
>
>
> Any suggestions is appreciated,
>
> Thanks, Pasha
>
>
>
>
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>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 May 2009 23:50:38 -0700 (PDT)
> From: hannah pamela tan <hpdiamantetan at yahoo.com>
> Subject: [Dock-fans] dock 6.2 installation
> To: dock-fans at docking.org
> Message-ID: <704112.6776.qm at web111307.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Good day Sir/Ma'am!
> ?
> ?I'm Hannah and I'm working with the DOCK program for my undergraduate
> thesis. There was just a problem with the DOCK 6.2 installation. I was able
> to create the config.h file but an error occurred after I tried to execute
> the commands
> ?
> ?[user at dock ~] make all # builds all the DOCK programs
> ?[user at dock ~] make dock # builds only the dock program
> ?[user at dock ~] make utils # builds only the accessory programs
> ?
> ?Testing the executable(s) eventually produced an error.
> ?
> ?I hope you could help me. Thank you!
> ?
> ?
> ?Tan, Hannah
> ?BS Chemistry
> ?University of the Philippines?Los Banos
>
> Smile! ?Jesus loves yah!
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Wed, 27 May 2009 23:59:04 -0700 (PDT)
> From: hannah pamela tan <hpdiamantetan at yahoo.com>
> Subject: [Dock-fans] dock 6.2 installation
> To: dock-fans at docking.org
> Message-ID: <270508.72525.qm at web111310.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Good day Sir/Ma'am!
> ?
> ?I'm Hannah and I'm working with the DOCK program for my undergraduate
> thesis. There was just a problem with the DOCK 6.2 installation. I was able
> to create the config.h file but an error occurred after I tried to execute
> the commands
> ?
> ?[user at dock ~] make all # builds all the DOCK programs
> ?[user at dock ~] make dock # builds only the dock program
> ?[user at dock ~] make utils # builds only the accessory programs
> ?
> ?Testing the executable(s) eventually produced an error.
> ?
> ?I hope you could help me. Thank you!
> ?
> ?
> ?Tan, Hannah
> ?BS Chemistry
> ?University of the Philippines?Los Banos
>
> Smile! ?Jesus loves yah!
>
>
>
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>
> ------------------------------
>
> Message: 4
> Date: Thu, 28 May 2009 00:21:07 -0700 (PDT)
> From: hannah pamela tan <hpdiamantetan at yahoo.com>
> Subject: [Dock-fans] dock 6.2 installation
> To: dock-fans at docking.org
> Message-ID: <669072.26794.qm at web111306.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> > Good day Sir/Ma'am!
> >?
> > I'm Hannah and I'm working with the DOCK program for my undergraduate
> thesis. There was just a problem with the DOCK 6.2 installation. I was able
> to create the config.h file but an error occurred after I tried to execute
> the commands
> >?
> > [user at dock ~] make all # builds all the DOCK programs
> > [user at dock ~] make dock # builds only the dock program
> > [user at dock ~] make utils # builds only the accessory programs
> >?
> > Testing the executable(s) eventually produced an error.
> >?
> > I hope you could help me. Thank you!
> >?
> >?
> > Tan, Hannah
> > BS Chemistry
> > University of the Philippines?Los Banos
> >?
> > ____________________________________________
> > Smile!? Jesus loves yah!
> >?
>
> Smile! ?Jesus loves yah!
>
>
>
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> ------------------------------
>
> Message: 5
> Date: Thu, 28 May 2009 20:50:23 +1200
> From: Davide Mercadante <dmer018 at aucklanduni.ac.nz>
> Subject: [Dock-fans] problem g77 using ubuntu 9.04 and headers missing
>        for     dock executables
> To: dock-fans at docking.org
> Message-ID:
>        <1da69e140905280150r4b118a6ydb707eb5aba47053 at mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Dock-fans mailing list,
>
> I have tried to build the executables for DOCK6 and all its utilities after
> the creation of the configuration file (./configure gnu) using the command:
> make all.
>
> Unfortunately I was not able to create the executables because the machine
> gave me this error message:
>
> *The DOCK configuration file has been created.
> dmer018 at dmer018-laptop:~/Scrivania/dock6/install$ make all
> Starting installation of
> DOCK v6.2
> at gio mag 28 12:24:55 NZST 2009.
>
> cd ../src && make install
> make[1]: ingresso nella directory ?/home/dmer018/Scrivania/dock6/src?
> cd dock && make install
> make[2]: ingresso nella directory ?/home/dmer018/Scrivania/dock6/src/dock?
> g++ -c  -O2 -o amber_typer.o  amber_typer.cpp
> amber_typer.cpp: In function ?char* white_line(char*)?:
> amber_typer.cpp:15: error: ?strlen? was not declared in this scope
> amber_typer.cpp: In function ?int assign_node(ATOM_TYPE_NODE&, int)?:
> amber_typer.cpp:66: error: ?strtok? was not declared in this scope
> amber_typer.cpp:66: error: ?strcpy? was not declared in this scope
> amber_typer.cpp:87: error: ?strncmp? was not declared in this scope
> amber_typer.cpp: In function ?int check_type(const char*, const char*)?:
> amber_typer.cpp:125: error: ?strstr? was not declared in this scope
> amber_typer.cpp: In constructor ?ATOM_TYPE::ATOM_TYPE()?:
> amber_typer.cpp:251: error: ?INT_MIN? was not declared in this scope
> amber_typer.cpp: In member function ?void
> ATOM_TYPER::get_vdw_labels(std::string, bool)?:
> amber_typer.cpp:285: error: ?strncmp? was not declared in this scope
> amber_typer.cpp:346: error: ?strtok? was not declared in this scope
> amber_typer.cpp:382: error: ?INT_MIN? was not declared in this scope
> amber_typer.cpp:387: error: ?INT_MIN? was not declared in this scope
> amber_typer.cpp: In member function ?int
> ATOM_TYPER::assign_vdw_labels(DOCKMol&, int)?:
> amber_typer.cpp:475: error: ?strcmp? was not declared in this scope
> amber_typer.cpp: In member function ?void
> BOND_TYPER::get_flex_labels(std::string)?:
> amber_typer.cpp:531: error: ?strncmp? was not declared in this scope
> amber_typer.cpp:544: error: ?strlen? was not declared in this scope
> amber_typer.cpp:561: error: ?strtok? was not declared in this scope
> amber_typer.cpp: In member function ?void
> BOND_TYPER::get_flex_search(std::string)?:
> amber_typer.cpp:598: error: ?strtok? was not declared in this scope
> amber_typer.cpp:600: error: ?strcmp? was not declared in this scope
> amber_typer.cpp: In member function ?void
> CHEM_TYPER::get_chem_labels(std::string)?:
> amber_typer.cpp:753: error: ?strncmp? was not declared in this scope
> amber_typer.cpp:762: error: ?strtok? was not declared in this scope
> make[2]: *** [amber_typer.o] Errore 1
> make[2]: uscita dalla directory ?/home/dmer018/Scrivania/dock6/src/dock?
> make[1]: *** [dock6] Errore 2
> make[1]: uscita dalla directory ?/home/dmer018/Scrivania/dock6/src?
> make: *** [install] Errore 2
>
> *I have solved this problem inserting some heading missing in some of the
> files present in the folder ../dock6/src/dock/
>
> I list here the headers missing that I found hoping that someone cant ake
> advantage from the experience I had.
> The files to correct are:
>
> amber_typer.cpp ; conf_gen.cpp ; dockmol.cpp ; library_file.cpp ;
> orient.cpp
> ; score.cpp ; simplex.cpp ; sphere.cpp ; utils.cpp .*
>
> The header that need to be added are the following:
>
> amber_typer.cpp
>
> #include <stdio.h>
> #include <limits.h>
>
> conf_gen.cpp
>
> **#include <limits.h>
>
> dockmol.cpp
>
> #include <string.h>
>
> orient.cpp
>
> **#include <string.h>
>
> score.cpp
>
> #include <string.h>
>
> simplex.cpp
>
> #include <string.h>
>
> sphere.cpp
>
> #include <stdio.h>
> #include <string.h>
>
> utils.cpp
>
> #include <string.h>
>
> *Hope this can helps.*
>
> However, continuing the building of the executables in the phase of
> creation
> of the directories for the accessories I had the problem that the machine
> was not able to find the command g77.
> Obviously I tried to install the g77 compiler but with the ubuntu 9.04 (the
> release on which I am installing dock) I was not able to install it for a
> problem of unsolved dependencies that I was not able to solve.
>
> There is the possibility to continue the installation using another
> compiler?
> Please, anyone knows how I can solve this problem?
> Seems that g77 would be available only for the Hardy release of Ubuntu 7.10
> (also for the version 8.10 is not available but have been substituted by
> fort77).
>
> Thanks infinitely in advance for any advice.
>
> Cheers,
> Davide
>
> Davide Mercadante
> PhD Student - Department of Chemistry -
> Rm 438 ext. 89171
> Faculty of Science
> The University of Auckland
> Auckland, New Zealand
>
> *
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> End of Dock-fans Digest, Vol 60, Issue 24
> *****************************************
>



-- 
Prashant
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