shahid nayeem wrote:
Hi
When I run dssp alone with a .pdb file it works well. But when I run
with Gromacs as do_dssp it gives segmentation fault and does not do any
calculation except giving some intermediate files as follows.
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
Reading frame 0 time 0.000
Warning: if there are broken molecules in the trajectory file,
they can not be made whole without a run input file
What is your exact command line?
-Justin
Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#
Segmentation fault
shahid
On 5/18/10, *Justin A. Lemkul* <[email protected]
<mailto:[email protected]>> wrote:
shahid nayeem wrote:
Hi
After posting this mail I did some google search and after
changing the executible name to dssp I moved it in
/usr/local/bin/ After this when I did do_dssp it starts running
asks to select a group I choose main chain 5, then it generates
some intermediate file and gives error as segmentation fault. I
though this problem was because of the executible in
/usr/local/bin/ and rest of file in another directory say
/home/shahid/software/dssp/. For this first I set the path in
~/.bascrc
Other files should be irrelevant. The only file you need is the
dssp binary.
as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run
do_dssp I got the same intermediate file generated backing up
the previous one.
Intermediate files are not an issue. When the executable is in this
directory, does the calculation otherwise work?
Then I moved all the files of dssp directory to /usr/local/bin/
and then tried to run do_dssp I am in the same situation.
If the executable in your home directory structure works, but in
/usr/local/bin it fails, then it could be some sort of permission
error. It ultimately doesn't matter where your executable is,
/usr/local/bin is default, but you can set any other location you
like with the DSSP environment variable.
-Justin
waiting for your help
shahid nayeem
On 5/18/10, *Justin A. Lemkul* <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> wrote:
shahid nayeem wrote:
Dear All
I downloaded dsspcmbi.tar.gz, and compiled using command
./DsspCompileGCC as given in Readme.txt file. when I try
to run
do_dssp command in gromacs I get error
Well, what happened?
Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use
setenv
DSSP)
I checked for DSSP executible in /usr/local/bin/ and I
couldnt
find. I
It won't be there unless you put it there and you have
re-named it.
I believe the default name of the dssp program is
"dsspcmbi," which
you need to change when you move the executable.
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
-Justin
even tried dsspcmbi.zip file but again I got the same
error. I
compiled dssp as root. Now what shoul I do in order to
run do_dssp
comand of gromacs.
Shahid nayeem
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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