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.
a...@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 <[email protected]
<mailto:[email protected]>> 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?
a...@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
========================================
--
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