These were the exact commands used to install fftw 3.2.2<br> ./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared CC=cc F77=f77<br>make -j 48<br>make install<br><br>These were the exact commands used to install gromacs4.5.4<br>
./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3 --without-x --enable-float CC=gcc-4.3.2 CXX=g++-4.3.2 CFLAGS='-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -D_POSIX_PTHREAD_SEMANTICS'<br>
make -j 48<br>
make install<br><br>I had installed the gromacs version 4.5.3 earlier and encountered the same problem with pdb2gmx. Hence installed the latest version.<br>Thanks and Regards,<br>Raghu<br><br><br><div class="gmail_quote">
On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<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>
Ragothaman Yennamalli wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I had the issue of shared libraries while installing which I did troubleshoot and the installation went without any errors. I tried converting the pdb file to a new one using editconf and it runs perfectly fine. So, there is some issue with pdb2gmx, which I am not able to detect.<br>
Any hints will be appreciated.<br>
</blockquote>
<br></div>
Please provide the exact commands that you used to install Gromacs. What exactly were the issues that you had to circumvent? Have you installed previous versions of Gromacs that have worked, such that this problem is specific to 4.5.4?<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;"><div class="im">
Thanks and Regards,<br>
Raghu<br>
<br>
Subject: Re: [gmx-users] pdb2gmx segmentation fault<br></div>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
Message-ID: <<a href="mailto:4DAE452B.3090905@anu.edu.au" target="_blank">4DAE452B.3090905@anu.edu.au</a> <mailto:<a href="mailto:4DAE452B.3090905@anu.edu.au" target="_blank">4DAE452B.3090905@anu.edu.au</a>>><div class="im">
<br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:<br>
> Hi,<br>
> I have installed the latest version of gromacs 4.5.4 and the<br>
> installation went fine. When I run pdb2gmx I get Segmentation fault<br>
> even before I could select the force field options. I tried with<br>
> different pdb files and I get seg fault without any other error messages.<br>
> The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top<br>
<br>
Probably, no other GROMACS command works either, because of some shared<br>
library issue related to your new installation.<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
-- <br>
****************************************<br>
Ragothaman M Yennamalli, Ph.D.<br>
Postdoctoral Research Associate<br>
1012 Crop Genome Informatics Laboratory<br>
Department of Genetics, Development and Cell Biology<br>
Iowa State University<br>
Ames, Iowa 50011-3260 USA<br>
<br>
<a href="tel:%2B1%20515-294-8971" value="+15152948971" target="_blank">+1 515-294-8971</a> (Office)<br>
<a href="tel:%2B1%20515-294-8280" value="+15152948280" target="_blank">+1 515-294-8280</a> (Fax)<br>
<a href="tel:%2B1%20515-851-1016" value="+15158511016" target="_blank">+1 515-851-1016</a> (Mobile)<br>
<br>
"When you can do the common things of life in an uncommon way, you will command the attention of the world." -George Washington Carver<br>
<br>
</div><a href="http://www.public.iastate.edu/%7Eraghu/" target="_blank">http://www.public.iastate.edu/~raghu/</a> <<a href="http://www.public.iastate.edu/%7Eraghu/" target="_blank">http://www.public.iastate.edu/%7Eraghu/</a>><br>
<a href="http://www.artistrkrishnarao.com/" target="_blank">http://www.artistrkrishnarao.com/</a><br>
<br>
***************************************<br>
<br>
</blockquote>
<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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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</font></blockquote></div><br><br clear="all"><br>-- <br>****************************************<br>Ragothaman M Yennamalli, Ph.D.<br>Postdoctoral Research Associate<br>1012 Crop Genome Informatics Laboratory<br>Department of Genetics, Development and Cell Biology<br>
Iowa State University<br>Ames, Iowa 50011-3260 USA<br><br>+1 515-294-8971 (Office)<br>+1 515-294-8280 (Fax)<br>+1 515-851-1016 (Mobile)<br><br>"When
you can do the common things of life in an uncommon way, you will
command the attention of the world." -George Washington Carver<br><br><a href="http://www.public.iastate.edu/%7Eraghu/" target="_blank">http://www.public.iastate.edu/~raghu/</a><br><a href="http://www.artistrkrishnarao.com/" target="_blank">http://www.artistrkrishnarao.com/</a><br>
<br>***************************************<br><br>