[gmx-users] Re: segemntation fault after run do_dssp

[shika]

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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