Hi,<br><br>When I run the pdb2gmx, it is giving the error as folllowing. What can I do?<br><br>Thanks in advance<br><br><span style="color: rgb(204, 0, 0);">ab@ab-desktop:~/Masaüstü/gromacs-4.5.1/src/kernel$ pdb2gmx -h</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);">The program 'pdb2gmx' is currently not installed. You can install it by typing:</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">sudo apt-get install gromacs</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);">bash: pdb2gmx: command not found</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);"> -h</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">The program 'pdb2gmx' is currently not installed. You can install it by typing:</span><br style="color: rgb(204, 0, 0);">
<span style="color: rgb(204, 0, 0);">sudo apt-get install gromacs</span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">bash: pdb2gmx: command not found</span><br><br><br><div class="gmail_quote">02 Ekim 2010 02:08 tarihinde Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> yazdı:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Roland,<br>
<br>
Eventually I installed the installation steps with "./configure --prefix=$HOME/usr "as you said. can you send me the input file for test?<br>
I want to run a simulation. how can I do this?<br>
<br>
</blockquote>
<br></div>
Please do some tutorial material. I sent you the link before.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks for your helps<br>
<br>
<br>
2010/10/2 Roland Schulz <<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a> <mailto:<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>>><div class="im"><br>
<br>
Hi,<br>
<br>
either install as root by running:<br>
sudo make install<br>
<br>
or rerun the installation steps with ./configure --prefix=$HOME/usr<br>
to install it in your home directory.<br>
<br>
Roland<br>
<br>
2010/10/1 ahmet yıldırım <<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a><br></div>
<mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>>><div><div></div><div class="h5"><br>
<br>
Dear justin,<br>
<br>
Thanks for your reply. I did that you said. I tried to install<br>
Gromacs 4.5.1but I failed it. I enter this line "<br>
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install " in<br>
terminal. What can I do? I am sorry. I am a new user.<br>
<br>
Thanks in advance<br>
<br>
1. I installed fftw 3.2.2<br>
ab@ab-desktop:~/Masaüstü/ cd fftw-3.2.2<br>
ab@ab-desktop:~/Masaüstü/fftw-3.2.2<br>
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure<br>
--enable-threads --enable-float<br>
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 make<br>
ab@ab-desktop:~/Masaüstü/fftw-3.2.2 make install<br>
<br>
2. I tried to install Gromacs 4.5.1<br>
ab@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1<br>
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1<br>
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure<br>
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make<br>
ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install<br>
Making install in include<br>
make[1]: Entering directory<br>
`/home/ab/Masaüstü/gromacs-4.5.1/include'<br>
Making install in .<br>
make[2]: Entering directory<br>
`/home/ab/Masaüstü/gromacs-4.5.1/include'<br>
make[3]: Entering directory<br>
`/home/ab/Masaüstü/gromacs-4.5.1/include'<br>
make[3]: Nothing to be done for `install-exec-am'.<br>
test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p<br>
"/usr/local/gromacs/include/gromacs"<br>
/bin/mkdir: cannot create directory `/usr/local/gromacs':<br>
Permission denied<br>
make[3]: *** [install-pkgincludeHEADERS] Error 1<br>
make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'<br>
make[2]: *** [install-am] Error 2<br>
make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'<br>
make[1]: *** [install-recursive] Error 1<br>
make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include'<br>
make: *** [install-recursive] Error 1<br>
<br>
<br>
<br>
2010/10/1 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div></div>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div class="im"><br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Hi,<br>
<br>
I've installed GROMACS 4.0.3 and MPI libraries using<br>
Ubuntu 9.04 Synaptic Package Manager. What else should I do?<br>
I want to run a simulation in parallel on a single PC.<br>
Which commands should I enter the terminal?<br>
<br>
<br>
If I were you, I would uninstall this version (which is<br>
outdated by nearly 2 years!) and get version 4.5.1.<br>
Installing from source is quite easy. Not only will you<br>
benefit from hundreds of bug fixes and enhancements, but<br>
running in parallel on a multi-core machine is no longer<br>
MPI-dependent, making it somewhat easier.<br>
<br>
For usage and instructions, see the manual and any of the<br>
numerous tutorials linked here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials#General" target="_blank">http://www.gromacs.org/Documentation/Tutorials#General</a><br>
<br>
-Justin<br>
<br>
<br>
Thanks a lot for any instruction.<br>
<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>