[gmx-users] segemntation fault after run do_dssp

[Erik Marklund]

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 <pqah123 at gmail.com> 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 : syafiqahabdulghani at gmail.com @ GS33669 at mutiara.upm.edu.my
> -- 
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