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 <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 > > -- > 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 -- 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 -- 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