Justin A. Lemkul
jalemkul at vt.edu
Tue May 18 14:05:26 CEST 2010
shahid nayeem wrote:
> 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.
> waiting for your help
> shahid nayeem
> On 5/18/10, *Justin A. Lemkul* <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> 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.
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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