On 16/05/2012 5:33 PM, Sathish wrote:
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]
<mailto:[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]
<mailto:[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 (-:
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@localhost sathish]#
Am not clear to understand this problem. help me
--
--
Regards,
N. Sathishkumar,
<mailto:[email protected]>
On Wed, May 16, 2012 at 4:02 PM, Mark Abraham <[email protected]
<mailto:[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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