[gmx-users] gromacs synaptic package manager

ahmet yıldırım ahmedo047 at gmail.com
Sat Oct 2 14:20:54 CEST 2010


Hi,

When I run the pdb2gmx, it is giving the error as folllowing. What can I do?

Thanks in advance

ab at ab-desktop:~/Masaüstü/gromacs-4.5.1/src/kernel$ pdb2gmx -h
The program 'pdb2gmx' is currently not installed.  You can install it by
typing:
sudo apt-get install gromacs
bash: pdb2gmx: command not found
 -h
The program 'pdb2gmx' is currently not installed.  You can install it by
typing:
sudo apt-get install gromacs
bash: pdb2gmx: command not found


02 Ekim 2010 02:08 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Roland,
>>
>> Eventually I installed the installation steps with "./configure
>> --prefix=$HOME/usr "as you said. can you send me the input file for test?
>> I want to run a simulation. how can I do this?
>>
>>
> Please do some tutorial material.  I sent you the link before.
>
> -Justin
>
>  Thanks for your helps
>>
>>
>> 2010/10/2 Roland Schulz <roland at utk.edu <mailto:roland at utk.edu>>
>>
>>
>>    Hi,
>>
>>    either install as root by running:
>>    sudo make install
>>
>>    or rerun the installation steps with     ./configure --prefix=$HOME/usr
>>    to install it in your home directory.
>>
>>    Roland
>>
>>    2010/10/1 ahmet yıldırım <ahmedo047 at gmail.com
>>    <mailto:ahmedo047 at gmail.com>>
>>
>>
>>        Dear justin,
>>
>>        Thanks for your reply. I did that you said. I tried to install
>>        Gromacs 4.5.1but I failed it. I enter this line "
>>        ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make install " in
>>        terminal. What can I do? I am sorry. I am a new user.
>>
>>        Thanks in advance
>>
>>        1. I installed fftw 3.2.2
>>        ab at ab-desktop:~/Masaüstü/ cd fftw-3.2.2
>>        ab at ab-desktop:~/Masaüstü/fftw-3.2.2
>>        ab at ab-desktop:~/Masaüstü/fftw-3.2.2  ./configure
>>        --enable-threads --enable-float
>>        ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make
>>        ab at ab-desktop:~/Masaüstü/fftw-3.2.2 make install
>>
>>        2. I tried to install Gromacs 4.5.1
>>        ab at ab-desktop:~/Masaüstü/ cd gromacs-4.5.1
>>        ab at ab-desktop:~/Masaüstü/gromacs-4.5.1
>>        ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
>>        ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make
>>        ab at ab-desktop:~/Masaüstü/gromacs-4.5.1 make install
>>        Making install in include
>>        make[1]: Entering directory
>>        `/home/ab/Masaüstü/gromacs-4.5.1/include'
>>        Making install in .
>>        make[2]: Entering directory
>>        `/home/ab/Masaüstü/gromacs-4.5.1/include'
>>        make[3]: Entering directory
>>        `/home/ab/Masaüstü/gromacs-4.5.1/include'
>>        make[3]: Nothing to be done for `install-exec-am'.
>>        test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p
>>        "/usr/local/gromacs/include/gromacs"
>>        /bin/mkdir: cannot create directory `/usr/local/gromacs':
>>        Permission denied
>>        make[3]: *** [install-pkgincludeHEADERS] Error 1
>>        make[3]: Leaving directory
>> `/home/ab/Masaüstü/gromacs-4.5.1/include'
>>        make[2]: *** [install-am] Error 2
>>        make[2]: Leaving directory
>> `/home/ab/Masaüstü/gromacs-4.5.1/include'
>>        make[1]: *** [install-recursive] Error 1
>>        make[1]: Leaving directory
>> `/home/ab/Masaüstü/gromacs-4.5.1/include'
>>        make: *** [install-recursive] Error 1
>>
>>
>>
>>        2010/10/1 Justin A. Lemkul <jalemkul at vt.edu
>>        <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>
>>            ahmet yıldırım wrote:
>>
>>                Hi,
>>
>>                I've installed GROMACS 4.0.3 and MPI libraries using
>>                Ubuntu 9.04 Synaptic Package Manager. What else should I
>> do?
>>                I want to run a simulation in parallel on a single PC.
>>                Which commands should I enter the terminal?
>>
>>
>>            If I were you, I would uninstall this version (which is
>>            outdated by nearly 2 years!) and get version 4.5.1.
>>             Installing from source is quite easy.  Not only will you
>>            benefit from hundreds of bug fixes and enhancements, but
>>            running in parallel on a multi-core machine is no longer
>>            MPI-dependent, making it somewhat easier.
>>
>>            For usage and instructions, see the manual and any of the
>>            numerous tutorials linked here:
>>
>>            http://www.gromacs.org/Documentation/Tutorials#General
>>
>>            -Justin
>>
>>
>>                Thanks a lot for any instruction.
>>
>>
>>
>>            --             ========================================
>>
>>            Justin A. Lemkul
>>            Ph.D. Candidate
>>            ICTAS Doctoral Scholar
>>            MILES-IGERT Trainee
>>            Department of Biochemistry
>>            Virginia Tech
>>            Blacksburg, VA
>>            jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>            ========================================
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>>
>>
>>
>>        --         Ahmet YILDIRIM
>>
>>        --
>>
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>>
>>
>>
>>    --     ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>>    <http://cmb.ornl.gov>
>>
>>    865-241-1537, ORNL PO BOX 2008 MS6309
>>
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>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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>



-- 
Ahmet YILDIRIM
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