[gmx-users] DSSP

[Justin A. Lemkul]

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* <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> 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* <jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto: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/> <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

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