msnayeem at gmail.com
Tue May 18 15:49:45 CEST 2010
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#
On 5/18/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> shahid nayeem wrote:
>> 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
> 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.
> waiting for your help
>> shahid nayeem
>> On 5/18/10, *Justin A. Lemkul* <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> 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
>> 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.
>> 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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