[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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>> <mailto:gmx-users at gromacs.org>
>>
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>>
>>
>>
>>
>> -- Ahmet YILDIRIM
>>
>> --
>>
>> gmx-users mailing list gmx-users at gromacs.org
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>>
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>> <mailto:gmx-users-request at gromacs.org>.
>>
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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
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>>
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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
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Ahmet YILDIRIM
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