[gmx-users] DSSP

[Justin A. Lemkul]

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* <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
>         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
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

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

========================================