[gmx-users] pdb2gmx segmentation fault

[Ragothaman Yennamalli]

These were the exact commands used to install fftw 3.2.2
./configure  --prefix=/export/home/raghu/fftw --enable-float --enable-shared
CC=cc F77=f77
make -j 48
make install

These were the exact commands used to install gromacs4.5.4
./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'
make -j 48
make install

I had installed the gromacs version 4.5.3 earlier and encountered the same
problem with pdb2gmx. Hence installed the latest version.
Thanks and Regards,
Raghu


On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Ragothaman Yennamalli wrote:
>
>> 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.
>> Any hints will be appreciated.
>>
>
> 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?
>
> -Justin
>
>  Thanks and Regards,
>> Raghu
>>
>> Subject: Re: [gmx-users] pdb2gmx segmentation fault
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org <mailto:
>> gmx-users at gromacs.org>>
>> Message-ID: <4DAE452B.3090905 at anu.edu.au <mailto:
>> 4DAE452B.3090905 at anu.edu.au>>
>>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote:
>>  > Hi,
>>  > I have installed the latest version of gromacs 4.5.4 and the
>>  > installation went fine. When I run pdb2gmx I get Segmentation fault
>>  > even before I could select the force field options. I tried with
>>  > different pdb files and I get seg fault without any other error
>> messages.
>>  > The command is: pdb2gmx -f new.pdb -o conf.gro -p topol.top
>>
>> Probably, no other GROMACS command works either, because of some shared
>> library issue related to your new installation.
>>
>> Mark
>>
>>
>>
>>
>> --
>> ****************************************
>> Ragothaman M Yennamalli, Ph.D.
>> Postdoctoral Research Associate
>> 1012 Crop Genome Informatics Laboratory
>> Department of Genetics, Development and Cell Biology
>> Iowa State University
>> Ames, Iowa 50011-3260 USA
>>
>> +1 515-294-8971 (Office)
>> +1 515-294-8280 (Fax)
>> +1 515-851-1016 (Mobile)
>>
>> "When you can do the common things of life in an uncommon way, you will
>> command the attention of the world." -George Washington Carver
>>
>> http://www.public.iastate.edu/~raghu/ <
>> http://www.public.iastate.edu/%7Eraghu/>
>> http://www.artistrkrishnarao.com/
>>
>> ***************************************
>>
>>
> --
> ========================================
>
> 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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-- 
****************************************
Ragothaman M Yennamalli, Ph.D.
Postdoctoral Research Associate
1012 Crop Genome Informatics Laboratory
Department of Genetics, Development and Cell Biology
Iowa State University
Ames, Iowa 50011-3260 USA

+1 515-294-8971 (Office)
+1 515-294-8280 (Fax)
+1 515-851-1016 (Mobile)

"When you can do the common things of life in an uncommon way, you will
command the attention of the world." -George Washington Carver

http://www.public.iastate.edu/~raghu/
http://www.artistrkrishnarao.com/

***************************************
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