[gmx-users] DSSP configuration in Gromacs 4.5.5

[Mark Abraham]

On 16/05/2012 5:33 PM, Sathish wrote:
> Dear Sir,
>
>          Thank u for reply and the old dssp executable was working fine,
>
>
> [root at localhost]# dssp
> COPYRIGHT
>   W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
>   CMBI version by Elmar.Krieger at cmbi.ru.nl 
> <mailto:Elmar.Krieger at cmbi.ru.nl> / April 1, 2010
> USAGE
>   dssp [Options] PDB_File DSSP_File -> Read PDB_File and write DSSP_File
>   dssp [Options] -- dssp_file       -> Read from stdin and write DSSP_File
>   dssp -h                           -> Display this help screen
> OPTIONS
>   -na   Disables the calculation of accessible surface.
>   -c    Classic (old) format.
>   -w    Wide 2002 format (for future use,not the current standard).
>   -v    Verbose.
>   --    Read from standard input.
>   -h -? Prints a help message.
>   -V    Prints version, as in first line of the output.
> ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS
>   By Emmanuel.Courcelle at toulouse.inra.fr 
> <mailto:Emmanuel.Courcelle at toulouse.inra.fr>
>   -ssa  Adds information about disulfide bonds to output file
>   -x    Renames residues with incomplete sidechains to 'X'
>   -alt2 Keeps an additional AltLoc indicator at the line ends
> [root at localhost]#
>
>
>   and i have checked one again the path of DSSP
>
> [root at localhost sathish]# echo $DSSP
> /usr/local/bin/dssp
> [root at localhost sathish]#
>
>
> but while running with do_dssp has problem.
>
>
> [root at localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx 
> -o ss.xpm
>                               :-)  G  R  O  M  A  C  S  (-:
>
>                                Grunge ROck MAChoS
>
>                   :-)  VERSION 4.5.5-dev-20120318-375fa98  (-:

You are not using 4.5.5. If you'd shown this the first time, you'd have 
used less of everybody's time. Maybe this version is one that is updated 
to use the new DSSP. Maybe you should go and use 4.5.5.

Also, don't do routine work logged in as root, unless you like 
reinstalling your whole operating system.

Mark

>     .
>     .
>     .
> Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single 
> precision)
> Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single 
> precision)
> Segmentation fault (core dumped)
> [root at localhost sathish]#
>
> Am not clear to understand this problem. help me
>
>
>
> -- 
> -- 
>
> Regards,
> N. Sathishkumar,
>
>
>
> <mailto:sathish at khu.ac.kr>
>
>
>
>
>
>
>
>
>
> On Wed, May 16, 2012 at 4:02 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 16/05/2012 4:54 PM, Sathish wrote:
>
>         Dear all,
>
>         How to install DSSP in Gromacs 4.5.5.
>
>         i set environmental variable "export DSSP=/usr/local/bin/dssp"
>         and checked.
>
>         I have refereed many posts related to dssp issue and tried
>         with new and old dssp executable but confused.
>         While running i got error " Segmentation fault".
>         Help me to solve this problem.
>
>
>     There's really nothing much that can be said beyond what is in
>     do_dssp -h. If the above environment variable points to a valid
>     old-style DSSP executable (does it? does it run?) then do_dssp
>     should work.
>
>     Mark
>     -- 
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>

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