[gmx-users] resolved pdm2gmx

Mark Abraham mark.abraham at anu.edu.au
Mon Oct 4 10:05:24 CEST 2010

----- Original Message -----
From: ahmet yıldırım <ahmedo047 at gmail.com>
Date: Monday, October 4, 2010 18:41
Subject: [gmx-users] resolved pdm2gmx
To: Discussion list for GROMACS users <gmx-users at 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
>     	 	 	 	  > 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
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


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