Dear Sir,
Thank u for reply and the old dssp executable was working fine,
[root@localhost]# dssp
COPYRIGHT
W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
CMBI version by [email protected] / 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 [email protected]
-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@localhost]#
and i have checked one again the path of DSSP
[root@localhost sathish]# echo $DSSP
/usr/local/bin/dssp
[root@localhost sathish]#
but while running with do_dssp has problem.
[root@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 (-:
.
.
.
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@localhost sathish]#
Am not clear to understand this problem. help me
--
--
Regards,
N. Sathishkumar,
<[email protected]>
On Wed, May 16, 2012 at 4:02 PM, Mark Abraham <[email protected]>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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