[gmx-users] do_dssp Segmentation fault

[Erik Marklund]

Hi,

The explanation is that DSSP changed its syntax some time ago and do_dssp no longer complied. More recent versions of do_dssp follows the new syntax  while still supporting the old one.

Erik

12 nov 2012 kl. 10.55 skrev João Henriques:

> Hello,
> 
> do_dssp (4.5.5) is broken. There are two possible answers you're gonna get
> here:
> 
> 1) Use old dssp, which you are using.
> 2) You're an idiot, which are not.
> 
> What I did to solve the problem was, download gmx from git, and substitute
> the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version.
> Re-compile it and voila! This do_dssp version accepts both old and new dssp
> and you have to specify which version with the flag -ver if I remember
> correctly.
> 
> This worked perfectly for me. I hope it helps you as well.
> 
> All the best,
> João Henriques
> 
> On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 <mshappy1986 at 126.com> wrote:
> 
>> Hi all,
>>   I am meeting the following error in Gromacs 4.5.5 with do_dssp
>>   Here is the command
>>       do_dssp -f md.xtc -s md.tpr -o dssp.xpm
>>  give me the following error
>>   segmentation fault
>>  I have downloaded the executable DSSP form
>> http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but
>> do_dssp did not work.
>>  How can I fix it?
>>  Thanks a lot
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> --
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> 
> 
> 
> -- 
> João Henriques
> --
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html