[gmx-users] resolved pdm2gmx

[ahmet yıldırım]

Dear Dr. Abraham,

I have been trying to install gromacs-4.5.1 for a week but I could not it. I
review the installation instructions step by step, but I failed again.

*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

*In this way, Gromacs-4.5.1 installed /usr/local/gromacs directory-(I have
root permissions to write there)*
*
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

*In this way, FFTW-3.2.2 installed /usr/local/include **and  **/usr/local/bin
**directories*-*-(I have root permissions to write there)*

You said:

> 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.
>
Can you tell me my mistake?

Please help me?

Sincerely yours


2010/10/4 Mark Abraham <mark.abraham at anu.edu.au>

>
>
> ----- 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
>
> Mark
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-- 
Ahmet YILDIRIM
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