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]>> 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/> | (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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