[gmx-users] dodssp segmentation fault SOLVED for DEBIAN

[Erik Marklund]

This issue has been resolved so the next official release of gromacs will be capacle of using the newer versions of dssp.

Erik

14 jun 2012 kl. 12.57 skrev Denis Kazakiewicz:

> Wow, just did that.
> In Debian have to use 4.5.5-2 version of Gromacs from sid repository.
> Still have to use the oldest dssp
> http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
> 
> It was simply Gromacs issue with no ways around.
> And it woks:)
> 
> Just wondering,
> What are other efficient ways of analyzing secondary structure instead of dssp? (novice question)
> Good luck to everybody
> 
> 
> On 14.06.2012 11:59, Denis Kazakiewicz wrote:
>> Hello
>> Dear Gromacs users.
>> This is many times discussed issue, however nothing seems to work so far
>> 
>> do_dssp returns "Segmentation fault"
>> 
>> It is the oldest version of dssp: dsspcmbi
>> Gromacs 4.5.5 on Debian i386
>> I did use export DSSP=/path to dssp
>> 
>> 1. What is possibly could be?
>> 2. Any other efficient ways of analyzing secondary structure without do_dssp (with VMD, may be)?
>> 
>> THANKS in advance
> 
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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

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