[gmx-users] DSSP

[Carsten Kutzner]

Hi,

there was a problem in do_dssp when used on proteins with more
than 10 chains. Is this the case? I just saw that I
only fixed that in the head, but not in 4.0.x.  

Carsten



On May 18, 2010, at 3:49 PM, 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
>  
>  
> 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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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne