Dear Dr. Abraham, I have been trying to install gromacs-4.5.1 for a week but I could not it. I review the installation instructions step by step, but I failed again.
*1.* I installed fftw-3.2.2 as following 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 *In this way, Gromacs-4.5.1 installed /usr/local/gromacs directory-(I have root permissions to write there)* * 2.* I installed gromacs-4.5.1 as folowing 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 sudo make install *In this way, FFTW-3.2.2 installed /usr/local/include **and **/usr/local/bin **directories*-*-(I have root permissions to write there)* You said: > This set of instructions will not use the above FFTW in GROMACS. The > configure command is inappropriate. Please see the installation guide for > the proper approach. > Can you tell me my mistake? Please help me? Sincerely yours 2010/10/4 Mark Abraham <mark.abra...@anu.edu.au> > > > ----- Original Message ----- > From: ahmet yıldırım <ahmedo...@gmail.com> > Date: Monday, October 4, 2010 18:41 > Subject: [gmx-users] resolved pdm2gmx > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Hi, > > > > I've written the Gromacs Mail list before, but I did not get the answer > that I wanted. I am new user Gromacs. > > > *> 1. I installed fftw-3.2.2 as following* > > > > > 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 installed gromacs-4.5.1 as folowing* > > > 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 sudo make install > > This set of instructions will not use the above FFTW in GROMACS. The > configure command is inappropriate. Please see the installation guide for > the proper approach. > > > *> "You need to either add the location of your Gromacs installation to > your PATH (in whatever shell configuration file, likely .bashrc) or source > GMXRC every time you log in to a new terminal. Once your Gromacs > installation is recognized by your shell environment you can run all the > commands."* > > I have read the installation instructions several times. > > I do not know how to apply what is said. > > This is a fairly basic UNIX issue, and has nothing specific to do with > GROMACS. You need to have an appreciation of what the UNIX environment is, > and how you can "source" a file to adjust that environment. Please look > around the web for some UNIX tutorial material - you'll need some experience > and knowledge here before you can do anything at all. Once you understand > the need to adjust the environment, you can see how "sourcing" GMXRC will > solve some of your problems. > > > > I have 1.pdb file. I want to convert 1.gro and 1.top this file using > pdb2gmx command. > > After this, what should I do? can you show me on the command? > *> pdb2gmx -f 1.pdb -o 1.gro -p 1.top* > > That's not really the purpose of pdb2gmx. It tries to generate a topology > from a set of coordinates. Perhaps working through some GROMACS tutorial > material is a good idea to get the beginnings of an understanding of the > workflows work. > > A file in specifically .gro format is not necessary at any point - see > http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file > > Mark > -- > 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