[gmx-users] pdb2gmx segmentation fault

[Justin A. Lemkul]

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
> 
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-- 
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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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