On 2010-10-03 23.16, ahmet yıldırım wrote:
Dear Prof. Spoel,
I am a Ph.D. student, Department of Physics, Harran University, Turkey.
I've written the Gromacs Mail list before, but I did not get the answer
that I wanted. I am new user Gromacs. I need your helps.
*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
/"*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 do not know how to apply what is said.
Put the following line in your .chsrc or .bash_profile files:
source /usr/local/bin/GMXRC
I have 1.pdb file. I want to convert 1.gro and 1.top this file using
pdb2gmx command.
a...@ab-desktop:~/usr/bin$ How do I go the following command from here?
After this, what should I do? can you show me on the command?
*pdb2gmx –f 1.pdb –o 1.gro –p 1.top*
Thanks in advance. Please, don't be angry with me.
--
Ahmet YILDIRIM
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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