[gmx-users] DSSP configuration in Gromacs 4.5.5

Sathish sathisbioinfo at gmail.com
Wed May 16 09:33:31 CEST 2012

Dear Sir,

         Thank u for reply and the old dssp executable was working fine,

[root at localhost]# dssp
  W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
  CMBI version by Elmar.Krieger at cmbi.ru.nl / April 1, 2010
  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
  -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.
  By 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
[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
                              :-)  G  R  O  M  A  C  S  (-:

                               Grunge ROck MAChoS

                  :-)  VERSION 4.5.5-dev-20120318-375fa98  (-:
Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single
Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single
Segmentation fault (core dumped)
[root at localhost sathish]#

Am not clear to understand this problem. help me


N. Sathishkumar,

<sathish at khu.ac.kr>

On Wed, May 16, 2012 at 4:02 PM, Mark Abraham <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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