[gmx-users] Re: resolved pdb2gmx

[Justin A. Lemkul]

As I said before, please keep all correspondence on the gmx-users list, for the 
benefit of the community, and perhaps the chance that someone else will have 
some helpful insight for you.

I do not know what else to tell you.  The instructions are very clear:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Getting_access_to_GROMACS_after_installation

Substitute the path to Gromacs from /usr/local/gromacs for wherever you 
installed the software on your system.

If you are unwilling or unable to attempt to follow the documentation, then 
there is likely no one who is going to continually offer you free help.

-Justin

ahmet yıldırım wrote:
>     Yes, so have you followed that advice?  You've given no indication
>     that you have.
> 
> 
> No, I haven't.
> I do not know how to apply your advices.
> 
> ab at ab-desktop:~/usr/bin$ How do I go the following command from here?
> pdb2gmx –f 1.pdb –o 1.gro –p 1.top
> 
> Thanks for your helps and patience
> 
> 02 Ekim 2010 16:44 tarihinde Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> yazdı:
> 
> 
>     Please keep all Gromacs-related correspondence on the gmx-users
>     list.  I am not a private tutor.
> 
>     See comments inline below.
> 
> 
>     ahmet yıldırım wrote:
> 
>         Hi,
> 
>         You said "Per the instructions I sent before, 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."
> 
> 
>     Yes, so have you followed that advice?  You've given no indication
>     that you have.
> 
>         I have 1.pdb file. I want to convert 1.gro and 1.top this file
>         using pdb2gmx command.
>         *pdb2gmx –f 1.pdb –o 1.gro –p 1.top*
> 
> 
>     That's the proper command, provided that the subdirectory containing
>     pdb2gmx is in your PATH, which you can accomplish by doing either of
>     the two things I have told you to do.
> 
> 
>         Can you give an example?
>         ab at ab-desktop:~/usr/bin$ .............?????
> 
> 
>     Sorry, I don't understand what you're asking for here.
> 
>     -Justin
> 
> 
>         Please, don't be angry with me.I am a Ph.D. student, Department
>         of Physics, Siirt University, Turkey.
>         Thanks in advance
>         -- 
>         Ahmet YILDIRIM
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================