[gmx-users] DSSP

[shahid nayeem]

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


Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#
Segmentation fault

shahid


On 5/18/10, Justin A. Lemkul <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>>
>> 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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