----- 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
