[gmx-users] pdb2gmx segmentation fault

Ragothaman Yennamalli ragothaman at gmail.com
Wed Apr 20 14:36:00 CEST 2011

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.
Thanks and Regards,

Subject: Re: [gmx-users] pdb2gmx segmentation fault
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <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.


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


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