Dear Dr. Abraham,<br><br>I have been trying to install gromacs-4.5.1 for a week but I could not it. <span id="result_box" class="" lang="en"><span style="" title=""> I review the installation instructions step by step</span></span><span id="result_box" class="" lang="en"><span style="" title="">, but I failed again</span></span>.<br>
<br><b>1.</b> I installed fftw-3.2.2 as following<br>
<p style="margin-bottom: 0cm;">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 --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</p><p style="margin-bottom: 0cm;"><b>In this way, Gromacs-4.5.1 installed /usr/local/gromacs directory-(I have root permissions to write there)</b></p>
<b><br>2.</b>
I installed
gromacs-4.5.1 as folowing
<p style="margin-bottom: 0cm;">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 sudo make install</p><br><b>In this way, FFTW-3.2.2 installed /usr/local/include </b><b>and </b><b>/usr/local/bin </b><b>directories</b>-<b>-(I have root permissions to write there)</b><br>
<br>You said:<br><blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">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.<br></blockquote><span id="result_box" class="short_text" lang="en"><span style="" title="">Can you tell me my mistake?</span></span><br><br>Please help me?<br><br>Sincerely yours<br><br><br><div class="gmail_quote">
2010/10/4 Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span><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>----- Original Message -----<br>From: ahmet yıldırım <<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>><br>Date: Monday, October 4, 2010 18:41<br>Subject: [gmx-users] resolved pdm2gmx<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><span lang="en"><span title=""><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi,<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I've written the Gromacs Mail list before, but I did not get the answer that I wanted</span></span>. I am new user Gromacs. <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><b><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>1. I installed fftw-3.2.2 as following</b><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> <p style="margin-bottom: 0cm;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/ cd fftw-3.2.2<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/fftw-3.2.2<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads --enable-float<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/fftw-3.2.2 make<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/fftw-3.2.2 make install</p>
<b><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>2. I installed gromacs-4.5.1 as folowing</b> <p style="margin-bottom: 0cm;">
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 make<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ab@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make install</p></div><p style="margin-bottom: 0cm;">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.<br>
</p><div class="im"><p style="margin-bottom: 0cm;"><br></p><i><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>"<b>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.</b>"</i> <span lang="en"><span title=""><br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have read the installation instructions several times.</span></span><br><span lang="en"><span title=""><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I do not know how to apply what is said.</span></span><br>
<br></div>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.<div class="im">
<br><br> <font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"></font><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have 1.pdb file. I want to convert 1.gro and 1.top this file using pdb2gmx command.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> After this, what should I do? can you show me on the command?<br> <b><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>pdb2gmx –f 1.pdb –o 1.gro –p 1.top</b><br>
<br></div>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.<br>
<br>A file in specifically .gro format is not necessary at any point - see <a href="http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file" target="_blank">http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file</a><br>
<font color="#888888"><br>Mark
</font><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>