[gmx-users] Re: pdb2gmx problem

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 4 14:18:16 CEST 2010

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*
> 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 installed  gromacs-4.5.1 as folowing*
> 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 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.
> ab at 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.
> --

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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