[gmx-users] resolved pdm2gmx

ahmet yıldırım ahmedo047 at gmail.com
Mon Oct 4 09:41:02 CEST 2010


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*

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
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 have read the installation instructions several times.
I do not know how to apply what is said.

I have 1.pdb file. I want to convert 1.gro and 1.top this file using pdb2gmx
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101004/d2996c35/attachment.html>

More information about the gromacs.org_gmx-users mailing list