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@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4dae452b.3090...@anu.edu.au
<mailto:4dae452b.3090...@anu.edu.au>>
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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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