[gmx-users] segemntation fault after run do_dssp

[Erik Marklund]

Hi,

It may very well be. Here's the red mine issue http://redmine.gromacs.org/issues/891. If there's a -ver option for do_dssp then it's capable of the new syntax. If not then it assumes the old syntax. If you can't install a newer version of gromacs there is the option to install old_dssp which is available through the dssp webpage.

Erik

On 7 Jun 2013, at 10:20, shika <pqah123 at gmail.com> wrote:

> Hi Eric,
> 
> I'm using gromacs 4.5.5.
> Is it the version is different for dssp?
> 
> Thanks
> 
> On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS]
> <ml-node+s5086n5008885h19 at n6.nabble.com> wrote:
>> HI,
>> 
>> What version of gromacs is this? DSSP changed its syntax a while back and we
>> had to adjust do_dssp accordingly. You may have a mismatch between gromacs
>> and dssp versions.
>> 
>> Erik
>> 
>> On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani <[hidden email]> wrote:
>> 
>>> Hi All,
>>> 
>>> I already done the MD production so I want to analyse the helical
>>> structure of my protein by using do_dssp program.The command is like
>>> below :
>>> 
>>> do_dssp -s md_water50.tpr -f md_water50.trr -n mainchain.ndx -sc
>>> dssp_scount.xvg -a dssp_area.xvg -ta dssp_totarea.xvg -aa
>>> dssp_averarea.xvg
>>> 
>>> but after i run the command the result show like :
>>> 
>>> Reading file md_water50.tpr, VERSION 4.5.5 (double precision)
>>> Reading file md_water50.tpr, VERSION 4.5.5 (double precision)
>>> Segmentation fault (core dumped)
>>> 
>>> 
>>> I already install the dssp program from
>>> ftp://ftp.cmbi.ru.nl/pub/software/dssp/ and follow the instruction as
>>> shown there but it seems that nothing happened..I already gedit the
>>> .bashrc for dssp.
>>> 
>>> --
>>> Best Regards,
>>> 
>>> Nur Syafiqah Abdul Ghani,
>>> Theoretical and Computational Chemistry Laboratory,
>>> Department of Chemistry,
>>> Faculty of Science,
>>> Universiti Putra Malaysia,
>>> 43400 Serdang,
>>> Selangor.
>>> alternative email : [hidden email] @ [hidden email]
>>> --
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> 
> 
> 
> -- 
> Best Regards,
> 
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> alternative email : syafiqahabdulghani at gmail.com @ GS33669 at mutiara.upm.edu.my
> 
> 
> 
> 
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