Hi, When I run the pdb2gmx, it is giving the error as folllowing. What can I do?
Thanks in advance a...@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 <jalem...@vt.edu> yazdı: > > > ahmet yıldırım wrote: > >> Dear Roland, >> >> Eventually I installed the installation steps with "./configure >> --prefix=$HOME/usr "as you said. can you send me the input file for test? >> I want to run a simulation. how can I do this? >> >> > Please do some tutorial material. I sent you the link before. > > -Justin > > Thanks for your helps >> >> >> 2010/10/2 Roland Schulz <rol...@utk.edu <mailto:rol...@utk.edu>> >> >> >> Hi, >> >> either install as root by running: >> sudo make install >> >> or rerun the installation steps with ./configure --prefix=$HOME/usr >> to install it in your home directory. >> >> Roland >> >> 2010/10/1 ahmet yıldırım <ahmedo...@gmail.com >> <mailto:ahmedo...@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 " >> a...@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 >> a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure >> --enable-threads --enable-float >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install >> >> 2. I tried to install Gromacs 4.5.1 >> a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make >> a...@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 <jalem...@vt.edu >> <mailto:jalem...@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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Ahmet YILDIRIM >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- 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@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> 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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists