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 <[email protected]> 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* <[email protected] <mailto:[email protected]>> >> 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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 [email protected] > 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 [email protected]. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
