[gmx-users] Re: pdb2gmx: segmentation fault

[Justin A. Lemkul]

Kwee Hong wrote:
> Sorry. Sorry.
> This would be the working one. I've tested it outside my uni domain.
> 
> http://www.birg1.fbb.utm.my/joyce/protein_dock.pdb 

Remove the www and it works for me.

Your .pdb file has several problems:

1. Loads of blank space at the end.
2. All lines are misformatted, with all columns after the chain identifier 
shifted by one space.  In vi, use :1,$s/ B / B/g to fix it.  This alleviates the 
seg fault.
3. Asn106 has its N atom labeled as residue 105.

Fixing all of the above resulted in a usable topology with Gromacs 4.5.3.

-Justin

> <http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb> 
> 
> joyce
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Friday, January 14, 2011 11:57:01
> *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault
> 
> 
> 
> Kwee Hong wrote:
>  > Sorry, this should be correct link to download the file.
>  >>
>  >> http://www.birg1.bioscience.utm.my/joyce/protein_dock.pdb
> 
> This link also does not work.
> 
> -Justin
> 
>  >> <http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb>
>  >>
>  >>
>  > Joyce
>  >
>  > ------------------------------------------------------------------------
>  > *From:* Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
>  > *Sent:* Friday, January 14, 2011 11:29:45
>  > *Subject:* Re: [gmx-users] Re: pdb2gmx: segmentation fault
>  >
>  >
>  >
>  > On 01/14/11, *Kwee Hong * <jestan1985 at yahoo.com 
> <mailto:jestan1985 at yahoo.com>> wrote:
>  >>
>  >> Hi all,
>  >>
>  >> I've uploaded my pdb file
>  >> at http://www.birg1.bioscience.com.my/joyce/protein_dock.pdb
>  >> Maybe someone can help me to look into it and see does it has any error.
>  >>
>  > That link does not work.
>  >
>  > Mark
>  >>
>  >>
>  >
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

-- 
========================================

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

========================================