[gmx-users] DSSP
Carsten Kutzner
ckutzne at gwdg.de
Thu May 20 10:13:03 CEST 2010
Hi Shahid,
I have fixed the problem in do_dssp. You can either pull the
newest release-4-0-patches branch from the git repository
or change ./src/tools/do_dssp.c, line 80 from
snew(ssbuf,nres+10);
to:
snew(ssbuf, 2*nres-1);
Carsten
On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote:
> 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
>
>
>
>
> --
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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
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