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 <jalem...@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* <jalem...@vt.edu <mailto:jalem...@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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> 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-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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